[med-svn] [Git][med-team/bcbio][master] cnvkit executable now found without further ado

[Steffen Möller]

Steffen Möller pushed to branch master at Debian Med / bcbio


Commits:
50ace2d9 by Steffen Moeller at 2020-11-14T22:30:48+01:00
cnvkit executable now found without further ado

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/cnvkitPath.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,14 @@
+bcbio (1.2.4-3) UNELEASED; urgency=medium
+
+  * Compatibility with Python 3.9
+  * Rounded-up Debian experience
+    - Added runtime/testing build depdendencies
+    - Adjusted names of executables in Debian
+      + hts-nim-tools
+      + cnvkit
+
+ -- Steffen Moeller <moeller at debian.org>  Sat, 14 Nov 2020 22:29:00 +0100
+
 bcbio (1.2.4-2) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/control
=====================================
@@ -33,6 +33,7 @@ Build-Depends: debhelper-compat (= 13),
                grabix <!nocheck>,
                hisat2 <!nocheck>,
                hts-nim-tools <!nocheck>,
+               lumpy-sv <!nocheck>,
                mosdepth <!nocheck>,
                multiqc <!nocheck>,
                perl <!nocheck>,
@@ -95,6 +96,7 @@ Depends: ${python3:Depends},
          python3-tornado
 Recommends:
          cnvkit,
+         lumpy-sv,
          mosdepth,
          multiqc,
          python3-arrow,


=====================================
debian/patches/cnvkitPath.patch
=====================================
@@ -0,0 +1,58 @@
+Index: bcbio/bcbio/structural/cnvkit.py
+===================================================================
+--- bcbio.orig/bcbio/structural/cnvkit.py
++++ bcbio/bcbio/structural/cnvkit.py
+@@ -162,7 +162,7 @@ def _run_cnvkit_population(items, backgr
+             out.extend(_associate_cnvkit_out(ckouts, [cur_input]))
+         return out
+ 
+-def _get_cmd(script_name="cnvkit.py"):
++def _get_cmd(script_name="cnvkit"):
+     return os.path.join(os.path.dirname(os.path.realpath(sys.executable)), script_name)
+ 
+ def _prep_cmd(cmd, tx_out_file):
+@@ -493,7 +493,7 @@ def _add_seg_to_output(out, data, enumer
+     out_file = "%s.seg" % os.path.splitext(out["cns"])[0]
+     if not utils.file_exists(out_file):
+         with file_transaction(data, out_file) as tx_out_file:
+-            cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "export",
++            cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit"), "export",
+                    "seg"]
+             if enumerate_chroms:
+                 cmd += ["--enumerate-chroms"]
+@@ -542,7 +542,7 @@ def _add_variantcalls_to_output(out, dat
+     if not utils.file_exists(call_file):
+         with file_transaction(data, call_file) as tx_call_file:
+             filters = ["--filter", "cn"]
+-            cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "call"] + \
++            cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit"), "call"] + \
+                   filters + \
+                    ["--ploidy", str(ploidy.get_ploidy([data])),
+                     "-o", tx_call_file, out["cns"]]
+@@ -563,7 +563,7 @@ def _add_variantcalls_to_output(out, dat
+         calls[outformat] = out_file
+         if not os.path.exists(out_file):
+             with file_transaction(data, out_file) as tx_out_file:
+-                cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "export",
++                cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit"), "export",
+                        outformat, "--sample-id", dd.get_sample_name(data),
+                        "--ploidy", str(ploidy.get_ploidy([data])),
+                        "-o", tx_out_file, call_file]
+@@ -581,7 +581,7 @@ def _add_segmetrics_to_output(out, data)
+     out_file = "%s-segmetrics.txt" % os.path.splitext(out["cns"])[0]
+     if not utils.file_exists(out_file):
+         with file_transaction(data, out_file) as tx_out_file:
+-            cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "segmetrics",
++            cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit"), "segmetrics",
+                    "--median", "--iqr", "--ci", "--pi",
+                    "-s", out["cns"], "-o", tx_out_file, out["cnr"]]
+             # Use less fine grained bootstrapping intervals for whole genome runs
+@@ -599,7 +599,7 @@ def _add_gainloss_to_output(out, data):
+     out_file = "%s-gainloss.txt" % os.path.splitext(out["cns"])[0]
+     if not utils.file_exists(out_file):
+         with file_transaction(data, out_file) as tx_out_file:
+-            cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit.py"), "gainloss",
++            cmd = [os.path.join(os.path.dirname(sys.executable), "cnvkit"), "gainloss",
+                    "-s", out["cns"], "-o", tx_out_file, out["cnr"]]
+             gender = _get_batch_gender([data])
+             if gender:


=====================================
debian/patches/series
=====================================
@@ -6,3 +6,4 @@ do_not_use_git.patch
 pythonpaths.patch
 hts_nim_tools.patch
 collectionsAbc.patch
+cnvkitPath.patch



View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/50ace2d97dffa89c7175c39a1f0edf608f971443

-- 
View it on GitLab: https://salsa.debian.org/med-team/bcbio/-/commit/50ace2d97dffa89c7175c39a1f0edf608f971443
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