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<h3>
Steffen Möller pushed to branch master
at <a href="https://salsa.debian.org/med-team/bcbio">Debian Med / bcbio</a>
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<h4>
Commits:
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<strong><a href="https://salsa.debian.org/med-team/bcbio/commit/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd">ab7dd934</a></strong>
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<span>by Steffen Möller</span>
<i>at 2019-01-21T21:38:49Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Fine-tuning for first upload
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<h4>7 changed files:</h4>
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debian/README.Debian
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debian/bcbio.lintian-overrides
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<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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debian/control
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debian/manpages
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debian/python3-bcbio.lintian-overrides
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<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="f168b81935360ddcf2dd0f2d4b98b8603829060f">
<a href="https://salsa.debian.org/med-team/bcbio/commit/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd#f168b81935360ddcf2dd0f2d4b98b8603829060f"><strong>debian/README.Debian</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">bcbio-nextgen</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">=============</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">This package builds and tests fine, but the documentation is not yet packaged.</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Please be aware of related Debian packages for toil and cwltool.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> -- Steffen Moeller Mon, 21 Jan 2019 21:30:11 +0100</span></pre>
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<li id="6fcfe3c1349787fc686a74ff850b52d83b96554d">
<a href="https://salsa.debian.org/med-team/bcbio/commit/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd#6fcfe3c1349787fc686a74ff850b52d83b96554d"><strong>debian/bcbio.lintian-overrides</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"># Better not mess with the community that expects these binaries</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext"># just like they are.</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">bcbio: script-with-language-extension usr/bin/bcbio_fastq_umi_prep.py</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">bcbio: script-with-language-extension usr/bin/bcbio_nextgen.py</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">bcbio: script-with-language-extension usr/bin/bcbio_prepare_samples.py</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">bcbio: script-with-language-extension usr/bin/bcbio_setup_genome.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">bcbio: script-with-language-extension usr/bin/cwltool2wdl.py</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,4 +2,6 @@ bcbio (1.1.2-1) unstable; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * Initial release (Closes: #903386)</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> TODO: Documentation not built</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"> -- Steffen Moeller <moeller@debian.org> Thu, 17 Jan 2019 16:37:37 +0100</span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,9 +16,12 @@ Build-Depends: debhelper (>= 10),</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"> python3-pyvcf,</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> python3-toolz,</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> python3-tornado,</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> python3-yaml,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># for testing</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> python3-biopython,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> python3-cyvcf2,</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> python3-logbook</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> python3-logbook,</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> python3-requests</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">Standards-Version: 4.3.0</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/bcbio</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/bcbio.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,10 +32,8 @@ Architecture: all</td>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"> python3-seqcluster,</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> python3-tornado,</span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="plaintext"> python3-yaml</span>
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<pre style="margin: 0;">-<span id="LC34" class="line" lang="plaintext">Suggests: toil</span>
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<pre style="margin: 0;">-<span id="LC35" class="line" lang="plaintext">Description: toolkit for analysing high-throughput sequencing data</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> python3-tornado</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">Description: library for analysing high-throughput sequencing data</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="plaintext"> This package installs the Python 3 libraries of the bcbio-nextgen</span>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="plaintext"> toolkit implementing best-practice pipelines for fully automated high</span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="plaintext"> throughput sequencing analysis.</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -43,3 +44,21 @@ Description: toolkit for analysing high-throughput sequencing data</td>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="plaintext"> contributes a shared community resource that handles the data processing</span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="plaintext"> component of sequencing analysis, providing researchers with more time</span>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext"> to focus on the downstream biology.</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Package: bcbio</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">Architecture: all</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">Depends: ${python3:Depends},</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext"> ${misc:Depends},</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext"> python3-bcbio</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">Suggests: toil, cwltool</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">Description: toolkit for analysing high-throughput sequencing data</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> This package installs the command line tools of the bcbio-nextgen</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> toolkit implementing best-practice pipelines for fully automated high</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> throughput sequencing analysis.</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext"> .</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> A high-level configuration file specifies inputs and analysis parameters</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> to drive a parallel pipeline that handles distributed execution,</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> idempotent processing restarts and safe transactional steps. The project</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> contributes a shared community resource that handles the data processing</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext"> component of sequencing analysis, providing researchers with more time</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"> to focus on the downstream biology.</span></pre>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">debian/bcbio_fastq_umi_prep.py.1</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext">debian/bcbio_nextgen.py.1</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">debian/bcbio_nextgen_install.py.1</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">debian/bcbio_prepare_samples.py.1</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">debian/bcbio_setup_genome.py.1</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">debian/cwltool2wdl.py.1</span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd#a12961191db6d1edd22994f0dedda7cf12a1856c"><strong>debian/python3-bcbio.lintian-overrides</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext"># Better not mess with the community that expects these binaries</span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="plaintext"># just like they are.</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">python3-bcbio: script-with-language-extension usr/bin/bcbio_fastq_umi_prep.py</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext">python3-bcbio: script-with-language-extension usr/bin/bcbio_nextgen.py</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext">python3-bcbio: script-with-language-extension usr/bin/bcbio_prepare_samples.py</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">python3-bcbio: script-with-language-extension usr/bin/bcbio_setup_genome.py</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">python3-bcbio: script-with-language-extension usr/bin/cwltool2wdl.py</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/bcbio/commit/ab7dd9340ea3d8dd23d3fe1b2e29ad27b92283cd#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -10,20 +10,27 @@ export PYBUILD_NAME=bcbio</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">#override_dh_auto_test:</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"># echo "No testing."</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">override_dh_auto_install:<span class="idiff left right"> manpages</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">override_dh_auto_install:</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> dh_auto_install</span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> <span class="idiff left right">#[ -d debian/python-bcbio-bin ] && mkdir -p debian/python-bcbio-bin</span>/usr/bin</span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext"> <span class="idiff left right">#mkdir -p debian/python3-bcbio-bin/usr/bin</span></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> #<span class="idiff left right">[ -d debian/python-bcbio-bin/usr/bin ] && mv debian/python-bcbio/usr/bin/* debian/python-bcbio-bin/usr/bin </span></span>
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18
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> #m<span class="idiff left right">v debian/python3-bcbio/usr/bin/* debian/python3-bcbio-bin/usr/bin </span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> <span class="idiff left right">[ -d debian/bcbio ] && mkdir -p debian/bcbio</span>/usr/bin</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> <span class="idiff left right">mv debian/python3-bcbio/usr/bin/* debian/bcbio/usr/bin/</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> #<span class="idiff left right"> To keep awareness of redundant binaries with different versions of Python</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> #m<span class="idiff left right">kdir -p debian/bcbio/usr/bin</span></span>
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19
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19
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> #rm -rf debian/python-bcbio/usr/bin debian/python3-bcbio/usr/bin</span>
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20
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20
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> </span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"># Problem with a series of tools that need bcbio before it is installed,</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"># just to print --help</span>
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21
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23
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"></span>
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22
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24
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext">manpages: debian/bcbio_nextgen.1</span>
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23
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25
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext">debian/bcbio_nextgen.1: scripts/bcbio_nextgen.py</span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> mkdir -p debian/bcbio/usr/share/man/man1</span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> export PYTHONPATH=debian/usr/lib/python3/dist-packages ; \</span>
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24
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28
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="plaintext"> for py in scripts/*.py; do \</span>
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25
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> help2man -<span class="idiff left right">-no-discard-stderr -h $$py python > debian/$$(basename $$py).1</span> ; \</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> help2man -<span class="idiff left right">N -s 1 --no-discard-stderr -h $$py -n $$(basename $$py .py) python | gzip -c > debian/bcbio/usr/share/man/man1/$$(basename $$py).1.gz</span> ; \</span>
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26
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30
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> done</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext"> # problem with --help generation</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext"> find debian -name bcbio_fastq_umi_prep.py.1* -delete</span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> find debian -name bcbio_prepare_samples.py.1* -delete</span>
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27
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34
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<pre style="margin: 0;"> <span id="LC34" class="line" lang="plaintext"></span>
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28
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35
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="plaintext">override_dh_auto_clean:</span>
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29
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36
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="plaintext"> dh_auto_clean</span>
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