Nilesh Patra pushed to branch master at Debian Med / parsnp
Commits: 41fff01c by Nilesh Patra at 2020-10-01T17:24:21+05:30 Use raxmlHPC instead of raxmlHPC-PTHREADS - - - - - 2 changed files: - debian/changelog - debian/patches/proper_calls_to_tools.patch Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +parsnp (1.5.3+dfsg-2) UNRELEASED; urgency=medium + + * Team Upload. + * Use raxmlHPC instead of raxmlHPC-PTHREADS + + -- Nilesh Patra <[email protected]> Thu, 01 Oct 2020 17:23:41 +0530 + parsnp (1.5.3+dfsg-1) unstable; urgency=medium * Team Upload. ===================================== debian/patches/proper_calls_to_tools.patch ===================================== @@ -18,7 +18,7 @@ Description: Fix name of phipack executable # Check for dependencies missing = False - for exe in ["Profile", "raxmlHPC-PTHREADS", "harvesttools"]: -+ for exe in ["phipack-profile", "raxmlHPC-PTHREADS", "harvesttools"]: ++ for exe in ["phipack-profile", "raxmlHPC", "harvesttools"]: if shutil.which(exe) is None: missing = True logger.critical("{} not in system path!".format(exe)) @@ -62,3 +62,12 @@ Description: Fix name of phipack executable run_command(command) if not os.path.exists(os.path.join(outputDir, "parsnpAligner.xmfa")): +@@ -1366,7 +1366,7 @@ + break + if not use_fasttree: + with tempfile.TemporaryDirectory() as raxml_output_dir: +- command = "raxmlHPC-PTHREADS -m GTRCAT -p 12345 -T %d -s %s -w %s -n OUTPUT"%(threads,outputDir+os.sep+"parsnp.snps.mblocks", raxml_output_dir) ++ command = "raxmlHPC -m GTRCAT -p 12345 -T %d -s %s -w %s -n OUTPUT"%(threads,outputDir+os.sep+"parsnp.snps.mblocks", raxml_output_dir) + run_command(command) + os.system("mv {}/RAxML_bestTree.OUTPUT {}".format(raxml_output_dir, outputDir+os.sep+"parsnp.tree")) + View it on GitLab: https://salsa.debian.org/med-team/parsnp/-/commit/41fff01c444ecce01dd96c6273db468b32150850 -- View it on GitLab: https://salsa.debian.org/med-team/parsnp/-/commit/41fff01c444ecce01dd96c6273db468b32150850 You're receiving this email because of your account on salsa.debian.org.
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