[med-svn] [Git][med-team/parsnp][master] Use raxmlHPC instead of raxmlHPC-PTHREADS

[Nilesh Patra]

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 <npatra974 at gmail.com>  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
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