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 <[email protected]> -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 You're receiving this email because of your account on salsa.debian.org.
_______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
