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 <[email protected]> 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 You're receiving this email because of your account on salsa.debian.org.
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