Commit ab7dd934 authored by Steffen Möller's avatar Steffen Möller
Browse files

Fine-tuning for first upload

parent 0402c98e

debian/README.Debian

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bcbio-nextgen

=============



This package builds and tests fine, but the documentation is not yet packaged.



Please be aware of related Debian packages for toil and cwltool.



 -- Steffen Moeller   Mon, 21 Jan 2019 21:30:11 +0100

debian/bcbio.lintian-overrides

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# Better not mess with the community that expects these binaries

# just like they are.

bcbio: script-with-language-extension usr/bin/bcbio_fastq_umi_prep.py

bcbio: script-with-language-extension usr/bin/bcbio_nextgen.py

bcbio: script-with-language-extension usr/bin/bcbio_prepare_samples.py

bcbio: script-with-language-extension usr/bin/bcbio_setup_genome.py

bcbio: script-with-language-extension usr/bin/cwltool2wdl.py

debian/changelog

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@@ -2,4 +2,6 @@ bcbio (1.1.2-1) unstable; urgency=medium 


  * Initial release (Closes: #903386)



    TODO: Documentation not built



 -- Steffen Moeller <moeller@debian.org>  Thu, 17 Jan 2019 16:37:37 +0100

debian/control

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@@ -16,9 +16,12 @@ Build-Depends: debhelper (>= 10), 
               python3-pyvcf,

               python3-toolz,

               python3-tornado,

               python3-yaml,

# for testing

               python3-biopython,

               python3-cyvcf2,

               python3-logbook

               python3-logbook,

               python3-requests

Standards-Version: 4.3.0

Vcs-Browser: https://salsa.debian.org/med-team/bcbio

Vcs-Git: https://salsa.debian.org/med-team/bcbio.git
@@ -29,10 +32,8 @@ Architecture: all 
Depends: ${python3:Depends},

         ${misc:Depends},

         python3-seqcluster,

         python3-tornado,

         python3-yaml

Suggests: toil

Description: toolkit for analysing high-throughput sequencing data

         python3-tornado

Description: library for analysing high-throughput sequencing data

 This package installs the Python 3 libraries of the bcbio-nextgen

 toolkit implementing best-practice pipelines for fully automated high

 throughput sequencing analysis.
@@ -43,3 +44,21 @@ Description: toolkit for analysing high-throughput sequencing data 
 contributes a shared community resource that handles the data processing

 component of sequencing analysis, providing researchers with more time

 to focus on the downstream biology.



Package: bcbio

Architecture: all

Depends: ${python3:Depends},

         ${misc:Depends},

         python3-bcbio

Suggests: toil, cwltool

Description: toolkit for analysing high-throughput sequencing data

 This package installs the command line tools of the bcbio-nextgen

 toolkit implementing best-practice pipelines for fully automated high

 throughput sequencing analysis.

 .

 A high-level configuration file specifies inputs and analysis parameters

 to drive a parallel pipeline that handles distributed execution,

 idempotent processing restarts and safe transactional steps.  The project

 contributes a shared community resource that handles the data processing

 component of sequencing analysis, providing researchers with more time

 to focus on the downstream biology.

debian/manpages

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debian/bcbio_fastq_umi_prep.py.1

debian/bcbio_nextgen.py.1

debian/bcbio_nextgen_install.py.1

debian/bcbio_prepare_samples.py.1

debian/bcbio_setup_genome.py.1

debian/cwltool2wdl.py.1