Installs.

Source: bcbio

Section: unknown

Section: science

Priority: optional

Maintainer: Steffen Moeller <moeller@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>

 .

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.

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(

tests_variation_gatk_exception_handling.patch

structural_regions_scale_tupel.patch

postinst_errors.patch

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

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