Tag versions

Wscript-with-language-extension

The tag is present in Lintian version 2.114.68. That is the most recent version we know about.

We use semantic versions. The patch number is a commit step indicator relative to the 2.108.0 release tag in our Git repository.

You can find the detection logic for this version at commit a1e47cb. For merge requests, please use the latest version in the Lintian check files/scripts.

Visibility: warning

When scripts are installed into a directory in the system PATH, the script name should not include an extension such as .sh or .pl that denotes the scripting language currently used to implement it. The implementation language may change; if it does, leaving the name the same would be confusing and changing it would be disruptive.

For more information please consult:

Debian Policy Manual section 10.4

The following 130 source packages in the archive triggered the tag 430 times (in any Lintian version).

We found 336 overrides. The tag performed 22% of the time.

W usr/games/acm.tcl

allelecount

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/alleleCounter.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/alleleCounterToJson.pl

bamclipper

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bamclipper.sh

bcachefs-tools

W sbin/mount.bcachefs.sh

bcbio

- # Better not mess with the community that expects these binaries
- # just like they are.
O usr/bin/bcbio_fastq_umi_prep.py
- # Better not mess with the community that expects these binaries
- # just like they are.
O usr/bin/bcbio_nextgen.py
- # Better not mess with the community that expects these binaries
- # just like they are.
O usr/bin/bcbio_prepare_samples.py
- # Better not mess with the community that expects these binaries
- # just like they are.
O usr/bin/bcbio_setup_genome.py
- # Better not mess with the community that expects these binaries
- # just like they are.
O usr/bin/cwltool2wdl.py

bcftools

W usr/bin/color-chrs.pl
W usr/bin/gff2gff.py
W usr/bin/guess-ploidy.py
W usr/bin/plot-roh.py
W usr/bin/run-roh.pl
W usr/bin/vcfutils.pl

bind9-libs

O usr/bin/isc-config.sh

bindgraph

O usr/sbin/bindgraph.pl

biomaj3

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/biomaj_migrate_database.py

biomaj3-cli

W usr/bin/biomaj-cli.py

biomaj3-daemon

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/biomaj_daemon_consumer.py

biomaj3-download

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/biomaj_download_consumer.py

biomaj3-process

W usr/bin/biomaj_process_consumer.py

biomaj3-user

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/biomaj-users.py

bioperl-run

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bp_multi_hmmsearch.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bp_panalysis.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bp_papplmaker.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bp_run_neighbor.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bp_run_protdist.pl

bio-rainbow

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/select_all_rbcontig.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/select_best_rbcontig.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/select_best_rbcontig_plus_read1.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/select_sec_rbcontig.pl

- # cg3-autobin.pl is already widely used by tools building on CG-3,
- # so it would be quite messy to rename it
O usr/bin/cg3-autobin.pl

changeo

- # Ignoreing .py endings to preserve compatibility with
- # scripts exchanged in the community.
O usr/bin/AlignRecords.py
- # Ignoreing .py endings to preserve compatibility with
- # scripts exchanged in the community.
O usr/bin/AssignGenes.py
- # Ignoreing .py endings to preserve compatibility with
- # scripts exchanged in the community.
O usr/bin/BuildTrees.py
- # Ignoreing .py endings to preserve compatibility with
- # scripts exchanged in the community.
O usr/bin/ConvertDb.py
- # Ignoreing .py endings to preserve compatibility with
- # scripts exchanged in the community.
O usr/bin/CreateGermlines.py
- # Ignoreing .py endings to preserve compatibility with
- # scripts exchanged in the community.
O usr/bin/DefineClones.py
- # Ignoreing .py endings to preserve compatibility with
- # scripts exchanged in the community.
O usr/bin/MakeDb.py
- # Ignoreing .py endings to preserve compatibility with
- # scripts exchanged in the community.
O usr/bin/ParseDb.py

chip-seq

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/check_bed.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/chr_replace_sga.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/eland2sga.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/fps2sga.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/gff2sga.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/partit2bed.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/partit2gff.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/sga2fps.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/sga2gff.pl

cnvkit

W usr/bin/snpfilter.sh

condor

W usr/bin/condor_top.pl

couriergraph

W usr/sbin/couriergraph.pl

denss

W usr/bin/best_enantiomers.sh
W usr/bin/denss.align2xyz.py
W usr/bin/denss.align_and_average.py
W usr/bin/denss.align_by_principal_axes.py
W usr/bin/denss.align.py
W usr/bin/denss.all.py
W usr/bin/denss.average.py
W usr/bin/denss.calcfsc.py
W usr/bin/denss.fit_data.py
W usr/bin/denss.get_info.py
W usr/bin/denss.mrcops.py
W usr/bin/denss.pdb2mrc.py
W usr/bin/denss.py
W usr/bin/denss.refine.py
W usr/bin/denss.rho2dat.py
W usr/bin/fsc2res.py

direwolf

- # These are used with extensions in the example config and should be treated as well-known names
O usr/bin/dwespeak.sh
- # These are used with extensions in the example config and should be treated as well-known names
O usr/bin/telem-balloon.pl
- # These are used with extensions in the example config and should be treated as well-known names
O usr/bin/telem-bits.pl
- # These are used with extensions in the example config and should be treated as well-known names
O usr/bin/telem-data91.pl
- # These are used with extensions in the example config and should be treated as well-known names
O usr/bin/telem-data.pl
- # These are used with extensions in the example config and should be treated as well-known names
O usr/bin/telem-eqns.pl
- # These are used with extensions in the example config and should be treated as well-known names
O usr/bin/telem-parm.pl
- # These are used with extensions in the example config and should be treated as well-known names
O usr/bin/telem-seq.sh
- # These are used with extensions in the example config and should be treated as well-known names
O usr/bin/telem-unit.pl
- # These are used with extensions in the example config and should be treated as well-known names
O usr/bin/telem-volts.py

discosnp

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/run_discoSnp++_ML.sh
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/run_discoSnp++.sh

dnapi

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/dnapi.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/qual_offset.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/qual_trim.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/to_fasta.py

docbook-dsssl

O usr/bin/collateindex.pl

dpdk

- # upstream ships these, and changing them now would be backward incompatible
O usr/bin/dpdk-devbind.py
- # upstream ships these, and changing them now would be backward incompatible
O usr/bin/dpdk-hugepages.py
- # upstream ships these, and changing them now would be backward incompatible
O usr/bin/dpdk-pmdinfo.py
- # upstream ships it as such, avoid overrides that create incompatibility between distros
O usr/bin/dpdk-telemetry.py

drop-seq

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/create_Drop-seq_reference_metadata.sh
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/Drop-seq_alignment.sh
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/public_clp_template.sh

dvblast

W usr/bin/dvblast_mmi.sh

emboss

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/runJemboss.sh

gdal

- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdal2tiles.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdal2xyz.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdalattachpct.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdal_calc.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdalcompare.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdal_edit.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdal_fillnodata.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdal_merge.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdalmove.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdal_pansharpen.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdal_polygonize.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdal_proximity.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdal_retile.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/gdal_sieve.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/ogrmerge.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/pct2rgb.py
- # QGIS plugins rely on .py extension, see: http://hub.qgis.org/issues/9924
O usr/bin/rgb2pct.py

gettext

- # This is a shell function library, not a program to be run directly.
- # The name /usr/bin/gettext is already taken by gettext(1).
O usr/bin/gettext.sh

gfxreconstruct

- # Provided like this from upstream
O usr/bin/gfxrecon-capture.py
- # Provided like this from upstream
O usr/bin/gfxrecon.py

gjots2

W usr/bin/gjots2html.py

- # User scripts rely on the extension
O usr/bin/gmt_shell_functions.sh

gnome-common

W usr/bin/gnome-autogen.sh

gnuift

W usr/bin/gift-add-collection.pl
W usr/bin/gift-diagnose-print-all-ADI.pl
W usr/bin/gift-dtd-to-keywords.pl
W usr/bin/gift-dtd-to-tex.pl
W usr/bin/gift-mrml-client.pl
W usr/bin/gift-old-to-new-url2fts.pl
W usr/bin/gift-perl-example-server.pl
W usr/bin/gift-remove-collection.pl
W usr/bin/gift-start.pl
W usr/bin/gift-url-to-fts.pl

graphviz

W usr/bin/gvmap.sh

healpy

W usr/bin/healpy_get_wmap_maps.sh

hisat2

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/hisat2_extract_exons.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/hisat2_extract_snps_haplotypes_UCSC.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/hisat2_extract_snps_haplotypes_VCF.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/hisat2_extract_splice_sites.py

ifscheme

O sbin/wifichoice.sh

imdbpy

W usr/bin/s32imdbpy.py

kaptive

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/kaptive.py

kde-dev-scripts

- # Provided like this from upstream
O usr/bin/build-progress.sh
- # Provided like this from upstream
O usr/bin/fix-include.sh
- # Provided like this from upstream
O usr/bin/grantlee_strings_extractor.py
- # Provided like this from upstream
O usr/bin/kdelnk2desktop.py
- # Provided like this from upstream
O usr/bin/kdemangen.pl
- # Provided like this from upstream
O usr/bin/kde-systemsettings-tree.py
- # Provided like this from upstream
O usr/bin/png2mng.pl
- # Provided like this from upstream
O usr/bin/zonetab2pot.py

kdevelop

W usr/bin/kdevplatform_shell_environment.sh

O usr/bin/pykig.py

knockd

W usr/sbin/knock_helper_ipt.sh

kphotoalbum

- # shipped like this by upstream
O usr/bin/kpa-backup.sh
- # shipped like this by upstream
O usr/bin/open-raw.pl

lagan

- # Not messing with whatever defaults the community has already
- # established for maximal compatibility with existing scripts.
O usr/bin/anal_gloc.pl
- # Not messing with whatever defaults the community has already
- # established for maximal compatibility with existing scripts.
O usr/bin/lagan.pl
- # Not messing with whatever defaults the community has already
- # established for maximal compatibility with existing scripts.
O usr/bin/rechaos.pl
- # Not messing with whatever defaults the community has already
- # established for maximal compatibility with existing scripts.
O usr/bin/slagan-mfa.pl
- # Not messing with whatever defaults the community has already
- # established for maximal compatibility with existing scripts.
O usr/bin/slagan.pl
- # Not messing with whatever defaults the community has already
- # established for maximal compatibility with existing scripts.
O usr/bin/supermap.pl
- # Not messing with whatever defaults the community has already
- # established for maximal compatibility with existing scripts.
O usr/bin/xmfa2mfa.pl

lefse

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/lefse2circlader.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/lefse_format_input.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/lefse_plot_cladogram.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/lefse_plot_features.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/lefse_plot_res.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/lefse_run.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/qiime2lefse.py

libbio-db-ace-perl

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bp_process_wormbase.pl

libbio-samtools-perl

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bamToGBrowse.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/chrom_sizes.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/genomeCoverageBed.pl

libbio-searchio-hmmer-perl

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bp_hmmer_to_table.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bp_parse_hmmsearch.pl

libbio-tools-run-remoteblast-perl

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bp_remote_blast.pl

libcatalyst-perl

- # catalyst.pl is a well-known name, and it's unlikely that it will be
- # rewritten in any other language than perl
O usr/bin/catalyst.pl

libdevel-repl-perl

O usr/bin/re.pl

libhtml-formfu-perl

- # Helper script written in Perl.
- # Don't change the name, so users will not be confused (also the
- # implementation language will probably never change anyway)
O usr/bin/html_formfu_deploy.pl
- # Helper script written in Perl.
- # Don't change the name, so users will not be confused (also the
- # implementation language will probably never change anyway)
O usr/bin/html_formfu_dumpconf.pl

liblocale-maketext-lexicon-perl

- # Cf. http://bugs.debian.org/508505 and the discussion starting at
- # http://lists.debian.org/debian-devel/2008/12/msg00491.html ,
- # especially http://lists.debian.org/debian-devel/2008/12/msg00505.html
O usr/bin/xgettext.pl

libmason-perl

- # Upstream kindly renamed /usr/bin/mason to mason.pl due to clashes with a
- # file installed by the mason package. Being a utility for a Perl library,
- # the "current implementation" aspect of policy 10.4 doesn't apply.
O usr/bin/mason.pl

libmath-prime-util-perl

- # /usr/bin/factor is already part of coreutils. We leave this
- # called factor.pl to distinguish between them
O usr/bin/factor.pl

libstring-mkpasswd-perl

- # we leave the script as /usr/bin/mkpasswd.pl
- # because there is a /usr/bin/mkpasswd
O usr/bin/mkpasswd.pl

magics++

W usr/bin/metgram.sh

makedumpfile

W usr/bin/makedumpfile-R.pl

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/farm-run.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maq_eval.pl
- # Maq ships `maq' and `maq.pl', it is therefore not possible to rename `maq.pl'.
O usr/bin/maq.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maq_plot.pl

mesa

W usr/bin/mesa-overlay-control.py

metabat

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/aggregateBinDepths.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/aggregateContigOverlapsByBin.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/merge_depths.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/runMetaBat.sh

metaphlan2

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/add_metadata_tree.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/extract_markers.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/merge_metaphlan_tables.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/plot_tree_graphlan.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/read_fastx.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/sample2markers.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/strain_transmission.py

mimedefang

W usr/bin/graphdefang.pl
W usr/bin/mimedefang.pl
W usr/bin/watch-multiple-mimedefangs.tcl

minimap2

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/minimap2.py

mountpy

W usr/bin/mountpy.py

mtools

W usr/bin/amuFormat.sh

myspell

W usr/bin/is2my-spell.pl

nanopb

W usr/bin/nanopb_generator.py

netatalk

W usr/bin/asip-status.pl

netdata

W usr/sbin/netdata-claim.sh

neutron

W usr/bin/ovn_migration.sh

openmpi

W usr/bin/mpijavac.pl

opennebula-context

W usr/bin/onegate.rb

packmol

O usr/bin/solvate.tcl

pal2nal

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/pal2nal.pl

paraclu

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/paraclu-cut.sh

parallel

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/env_parallel.csh
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/env_parallel.sh

pfstools

W usr/bin/pfs_split_exposures.py

pftools

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/compare_2_profiles.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/fasta_to_fastq.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/make_iupac_cmp.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/ps_scan.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/scramble_fasta.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/sort_fasta.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/split_profile_file.pl

php-sabredav

W usr/bin/naturalselection.py

pizzly

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/flatten_json.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/get_fragment_length.py

plaso

- # We keep the names used in the upstream package because
- # - a lot of existing documentation depends on it
- # - /usr/bin/{pinfo,psort} have been taken by other packages
O usr/bin/image_export.py
- # We keep the names used in the upstream package because
- # - a lot of existing documentation depends on it
- # - /usr/bin/{pinfo,psort} have been taken by other packages
O usr/bin/log2timeline.py
- # We keep the names used in the upstream package because
- # - a lot of existing documentation depends on it
- # - /usr/bin/{pinfo,psort} have been taken by other packages
O usr/bin/pinfo.py
- # We keep the names used in the upstream package because
- # - a lot of existing documentation depends on it
- # - /usr/bin/{pinfo,psort} have been taken by other packages
O usr/bin/psort.py
- # We keep the names used in the upstream package because
- # - a lot of existing documentation depends on it
- # - /usr/bin/{pinfo,psort} have been taken by other packages
O usr/bin/psteal.py

presto

- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/AlignSets.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/AssemblePairs.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/BuildConsensus.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/ClusterSets.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/CollapseSeq.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/ConvertHeaders.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/EstimateError.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/FilterSeq.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/MaskPrimers.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/PairSeq.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/ParseHeaders.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/ParseLog.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/SplitSeq.py
- # Not addressed because of reverse dependencies on exactly those file
- # names in the community
O usr/bin/UnifyHeaders.py

prinseq-lite

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/prinseq-graphs-noPCA.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/prinseq-graphs.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/prinseq-lite.pl

proteinortho

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho2html.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho2tree.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho2xml.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho6.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho_compareProteinorthoGraphs.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho_do_mcl.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho_extract_from_graph.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho_ffadj_mcs.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho_formatUsearch.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho_grab_proteins.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho_history.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho_singletons.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/proteinortho_summary.pl

pychopper

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/cdna_classifier.py

pyftdi

O usr/bin/ftconf.py
O usr/bin/ftdi_urls.py
O usr/bin/i2cscan.py
O usr/bin/pyterm.py

python-bx

- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/aggregate_scores_in_intervals.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/align_print_template.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/axt_extract_ranges.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/axt_to_fasta.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/axt_to_lav.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/axt_to_maf.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_bigwig_profile.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_build_windows.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_complement.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_count_by_interval.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_count_overlapping.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_coverage_by_interval.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_coverage.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_diff_basewise_summary.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_extend_to.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_intersect_basewise.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_intersect.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_merge_overlapping.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_rand_intersect.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bed_subtract_basewise.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/bnMapper.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/div_snp_table_chr.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/find_in_sorted_file.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/gene_fourfold_sites.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/get_scores_in_intervals.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/interval_count_intersections.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/interval_join.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/int_seqs_to_char_strings.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/lav_to_axt.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/lav_to_maf.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/line_select.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/lzop_build_offset_table.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_build_index.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_chop.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_chunk.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_col_counts_all.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_col_counts.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_count.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_covered_ranges.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_covered_regions.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_div_sites.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_drop_overlapping.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_extract_chrom_ranges.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_extract_ranges_indexed.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_extract_ranges.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_filter_max_wc.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_filter.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_gap_frequency.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_gc_content.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_interval_alignibility.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_limit_to_species.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_mapping_word_frequency.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_mask_cpg.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_mean_length_ungapped_piece.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_percent_columns_matching.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_percent_identity.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_print_chroms.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_print_scores.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_randomize.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_region_coverage_by_src.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_select.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_shuffle_columns.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_species_in_all_files.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_split_by_src.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_thread_for_species.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_tile_2bit.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_tile_2.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_tile.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_to_axt.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_to_concat_fasta.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_to_fasta.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_to_int_seqs.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_translate_chars.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_truncate.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/maf_word_frequency.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/mask_quality.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/mMK_bitset.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/nib_chrom_intervals_to_fasta.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/nib_intervals_to_fasta.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/nib_length.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/one_field_per_line.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/out_to_chain.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/prefix_lines.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/pretty_table.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/qv_to_bqv.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/random_lines.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/table_add_column.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/table_filter.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/tfloc_summary.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/ucsc_gene_table_to_intervals.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/wiggle_to_array_tree.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/wiggle_to_binned_array.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/wiggle_to_chr_binned_array.py
- # Not fiddling with .py endings because of reverse-dependencies expected from toil
- # We shall revisit this decision once all packages for toil are in the distribution
- # and we have learned more about how bx is used in the community in 3rd party scripts.
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/wiggle_to_simple.py

python-cartopy

W usr/bin/cartopy_feature_download.py

python-enigma

- # this binary is a Python-only frontend to the library
O usr/bin/pyenigma.py

python-evtx

W usr/bin/evtx_dump_chunk_slack.py
W usr/bin/evtx_dump.py
W usr/bin/evtx_eid_record_numbers.py
W usr/bin/evtx_extract_record.py
W usr/bin/evtx_filter_records.py
W usr/bin/evtx_info.py
W usr/bin/evtx_record_structure.py
W usr/bin/evtx_structure.py
W usr/bin/evtx_templates.py

python-ipmi

- # Name conflicts with ipmitool and this is primarily a Python library
O usr/bin/ipmitool.py

python-jsonpath-rw

W usr/bin/jsonpath.py

python-pyani

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/average_nucleotide_identity.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/delta_filter_wrapper.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/genbank_get_genomes_by_taxon.py

pyxnat

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/sessionmirror.py

racon

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/racon_wrapper.py

rapmap

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/RunRapMap.sh

ruby-knapsack

W usr/bin/print_header.sh

ruby-license-finder

W usr/bin/license_finder_pip.py

ruby-redis-actionpack

W usr/bin/bundler-version-options.rb

ruby-stackprof

W usr/bin/stackprof-flamegraph.pl
W usr/bin/stackprof-gprof2dot.py

runawk

W usr/bin/alt_getopt.sh

samtools

- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/blast2sam.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/bowtie2sam.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/export2sam.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/fasta-sanitize.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/interpolate_sam.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/novo2sam.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/psl2sam.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/sam2vcf.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/samtools.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/seq_cache_populate.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/soap2sam.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/wgsim_eval.pl
- # Even if there is a conflict with Debian policy samtools internally
- # relies on these extensions (see #799698)
O usr/bin/zoom2sam.pl

sepp

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/run_sepp.py
- # The .sh one has a reverse dependency in q2-fragment-insertion
O usr/bin/run-sepp.sh

sg3-utils

W usr/bin/rescan-scsi-bus.sh

sibelia

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/C-Sibelia.py

snap

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/hmm-assembler.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/patch-hmm.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/zff2gff3.pl

snort

W usr/sbin/appid_detector_builder.sh

spirv-tools

W usr/bin/spirv-lesspipe.sh

ssft

O usr/bin/ssft.sh

starpu

W usr/bin/starpu_mpi_comm_matrix.py
W usr/bin/starpu_temanejo2.sh
W usr/bin/starpu_trace_state_stats.py

starpu-contrib

W usr/bin/starpu_mpi_comm_matrix.py
W usr/bin/starpu_temanejo2.sh
W usr/bin/starpu_trace_state_stats.py

syslinux

- # retained for compatibility with existing scripts
O usr/bin/isohybrid.pl

W usr/sbin/backup.sh

tcd-utils

W usr/bin/rewrite_tide_db.sh

tiddit

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/TIDDIT.py

tipp

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/run_abundance.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/run_tipp.py
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/run_tipp_tool.py

tophat-recondition

O usr/bin/tophat-recondition.py

trace2dbest

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/rename_file.pl
- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/trace2dbest.pl

- # see https://lists.debian.org/debian-med/2018/06/msg00043.html
O usr/bin/variant_caller_pipeline.py

unhide.rb

- # The extension is part of the name of the application
O usr/sbin/unhide.rb

wine-development

W usr/bin/function_grep.pl

xabacus

W usr/games/play.sh

xinetd

O usr/bin/xconv.pl