[med-svn] [Git][med-team/bcbio][master] Installs.
Steffen Möller
gitlab at salsa.debian.org
Sun Feb 11 19:34:02 UTC 2018
Steffen Möller pushed to branch master at Debian Med / bcbio
Commits:
018c4d85 by Steffen Moeller at 2018-02-11T20:33:47+01:00
Installs.
- - - - -
5 changed files:
- debian/control
- + debian/patches/postinst_errors.patch
- + debian/patches/series
- + debian/patches/structural_regions_scale_tupel.patch
- + debian/patches/tests_variation_gatk_exception_handling.patch
Changes:
=====================================
debian/control
=====================================
--- a/debian/control
+++ b/debian/control
@@ -1,20 +1,29 @@
Source: bcbio
-Section: unknown
+Section: science
Priority: optional
Maintainer: Steffen Moeller <moeller at debian.org>
-Build-Depends: debhelper (>= 10), dh-python, python-all, python-setuptools, python3-all, python3-setuptools
-Standards-Version: 4.1.2
-Homepage: <insert the upstream URL, if relevant>
+Build-Depends: debhelper (>= 10),
+ dh-python, python-all, python-setuptools, python3-all, python3-setuptools,
+ python3-toolz,
+ python-logbook, python3-logbook,
+ python-pysam, python3-pysam,
+ python3-pybedtools,
+ python3-gffutils,
+ python-cyvcf2, python3-cyvcf2,
+ python-pyvcf, python3-pyvcf,
+ python-pandas, python3-pandas
+Standards-Version: 4.1.3
+Homepage: https://github.com/chapmanb/bcbio-nextgen
X-Python-Version: >= 2.6
X-Python3-Version: >= 3.2
-#Vcs-Git: https://anonscm.debian.org/git/python-modules/packages/bcbio.git
-#Vcs-Browser: https://anonscm.debian.org/cgit/python-modules/packages/bcbio.git/
+Vcs-Git: https://salsa.debian.org/med-team/bcbio
+Vcs-Browser: https://salsa.debian.org/med-team/bcbio
#Testsuite: autopkgtest-pkg-python
Package: python-bcbio
Architecture: all
Depends: ${python:Depends}, ${misc:Depends}
-Suggests: python-bcbio-doc
+#Suggests: python-bcbio-doc
Description: <insert up to 60 chars description> (Python 2)
<insert long description, indented with spaces>
.
@@ -23,17 +32,17 @@ Description: <insert up to 60 chars description> (Python 2)
Package: python3-bcbio
Architecture: all
Depends: ${python3:Depends}, ${misc:Depends}
-Suggests: python-bcbio-doc
+#Suggests: python-bcbio-doc
Description: <insert up to 60 chars description> (Python 3)
<insert long description, indented with spaces>
.
This package installs the library for Python 3.
-Package: python-bcbio-doc
-Architecture: all
-Section: doc
-Depends: ${sphinxdoc:Depends}, ${misc:Depends}
-Description: <insert up to 60 chars description> (common documentation)
- <insert long description, indented with spaces>
- .
- This is the common documentation package.
+#Package: python-bcbio-doc
+#Architecture: all
+#Section: doc
+#Depends: ${sphinxdoc:Depends}, ${misc:Depends}
+#Description: <insert up to 60 chars description> (common documentation)
+# <insert long description, indented with spaces>
+# .
+# This is the common documentation package.
=====================================
debian/patches/postinst_errors.patch
=====================================
--- /dev/null
+++ b/debian/patches/postinst_errors.patch
@@ -0,0 +1,26 @@
+Index: bcbio/bcbio/pipeline/sra.py
+===================================================================
+--- bcbio.orig/bcbio/pipeline/sra.py
++++ bcbio/bcbio/pipeline/sra.py
+@@ -41,7 +41,7 @@ def query_gsm(gsm, out_file, config = {}
+ logger.debug("Get id sample for %s" % gsm)
+ if ids:
+ gsm_info = _query_info("sra", ids[-1])
+- print gsm_info
++ print(gsm_info)
+ srrall = []
+ for srr in gsm_info:
+ srrall.append(_create_link(srr))
+Index: bcbio/bcbio/qc/srna.py
+===================================================================
+--- bcbio.orig/bcbio/qc/srna.py
++++ bcbio/bcbio/qc/srna.py
+@@ -44,7 +44,7 @@ def _get_stats_from_miraligner(fn, out_f
+ version = get_version_manifest("seqbuster")
+ with file_transaction(out_file) as tx_out:
+ with open(tx_out, "w") as out_handle:
+- print >>out_handle, "# stats {name}, version: {version}".format(**locals())
++ print >>out_handle,("# stats {name}, version: {version}").format(**locals())
+ print >>out_handle, ("mirs\t{mirs}\nisomirs\t{isomirs}").format(
+ mirs=len(dfmirs.index), isomirs=len(df.index))
+ print >>out_handle, ("mirs_mutations\t{muts}\nmirs_additions\t{add}").format(
=====================================
debian/patches/series
=====================================
--- /dev/null
+++ b/debian/patches/series
@@ -0,0 +1,3 @@
+tests_variation_gatk_exception_handling.patch
+structural_regions_scale_tupel.patch
+postinst_errors.patch
=====================================
debian/patches/structural_regions_scale_tupel.patch
=====================================
--- /dev/null
+++ b/debian/patches/structural_regions_scale_tupel.patch
@@ -0,0 +1,15 @@
+Index: bcbio/bcbio/structural/regions.py
+===================================================================
+--- bcbio.orig/bcbio/structural/regions.py
++++ bcbio/bcbio/structural/regions.py
+@@ -89,7 +89,9 @@ class MemoizedSizes:
+ if r.stop - r.start > range_map["target"][1]:
+ anti_bps.append(float(r.name))
+ checked_beds.add(region_bed)
+- def scale_in_boundary(raw, round_interval, (min_val, max_val)):
++ def scale_in_boundary(raw, round_interval, tupel):
++ min_val=tupel[0]
++ max_val=tupel[1]
+ out = int(math.ceil(raw / float(round_interval)) * round_interval)
+ if out > max_val:
+ return max_val
=====================================
debian/patches/tests_variation_gatk_exception_handling.patch
=====================================
--- /dev/null
+++ b/debian/patches/tests_variation_gatk_exception_handling.patch
@@ -0,0 +1,13 @@
+Index: bcbio/bcbio/variation/gatk.py
+===================================================================
+--- bcbio.orig/bcbio/variation/gatk.py
++++ bcbio/bcbio/variation/gatk.py
+@@ -166,7 +166,7 @@ def haplotype_caller(align_bams, items,
+ try:
+ broad_runner.run_gatk(params, os.path.dirname(tx_out_file), memscale=memscale,
+ parallel_gc=_use_spark(num_cores, gatk_type))
+- except subprocess.CalledProcessError, msg:
++ except (subprocess.CalledProcessError, msg):
+ # Spark failing on regions without any reads, write an empty VCF instead
+ # https://github.com/broadinstitute/gatk/issues/4234
+ if (_use_spark(num_cores, gatk_type) and
View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/018c4d8562c64f53ad1c175ee0d3258da58ecb5b
---
View it on GitLab: https://salsa.debian.org/med-team/bcbio/commit/018c4d8562c64f53ad1c175ee0d3258da58ecb5b
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