[med-svn] [Git][med-team/trinityrnaseq][master] 3 commits: Attempt to fix STAR test error

[Michael R. Crusoe]

Michael R. Crusoe pushed to branch master at Debian Med / trinityrnaseq


Commits:
8f89a482 by Michael R. Crusoe at 2020-10-12T14:36:42+02:00
Attempt to fix STAR test error

- - - - -
f842ea4f by Michael R. Crusoe at 2020-10-12T15:16:49+02:00
skip the STAR DTU test until a better fix is found

- - - - -
56b1eb8a by Michael R. Crusoe at 2020-10-12T15:17:04+02:00
release 2.11.0+dfsg-2

- - - - -


4 changed files:

- debian/changelog
- + debian/patches/STAR_genomeSAindexNbases
- debian/patches/series
- + debian/patches/skip_DTU_STAR_test


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,11 @@
+trinityrnaseq (2.11.0+dfsg-2) unstable; urgency=medium
+
+  * debian/patches/STAR_genomeSAindexNbases: Attempt to fix the DTU STAR test error
+  * debian/patches/skip_DTU_STAR_test: skip the test until a better fix is
+    found
+
+ -- Michael R. Crusoe <crusoe at debian.org>  Mon, 12 Oct 2020 15:16:52 +0200
+
 trinityrnaseq (2.11.0+dfsg-1) unstable; urgency=medium
 
   [ Andreas Tille ]


=====================================
debian/patches/STAR_genomeSAindexNbases
=====================================
@@ -0,0 +1,21 @@
+From: Michael R. Crusoe <crusoe at debian.org>
+Subject: Implement genomeSAindexNbases
+Forwarded: https://github.com/trinityrnaseq/trinityrnaseq/issues/905#issuecomment-707094332
+--- trinityrnaseq.orig/util/misc/run_STAR_via_samples_file.pl
++++ trinityrnaseq/util/misc/run_STAR_via_samples_file.pl
+@@ -88,6 +88,7 @@
+     }
+ 
+     my $genomeChrBinNbits = min(18, int(log((-s $genome) / $num_contigs) / log(2) + 0.5) );
++    my $genomeSAindexNbases = int(log(-s $genome) / log(2) / 2) - 1;
+     
+     my @read_sets = &parse_samples_file($samples_file);    
+ 
+@@ -102,6 +103,7 @@
+     my $cmd = "$star_prog --runThreadN $CPU --runMode genomeGenerate --genomeDir $star_index "
+         . " --genomeFastaFiles $genome "
+         . " --genomeChrBinNbits $genomeChrBinNbits "
++        . " --genomeSAindexNbases $genomeSAindexNbases "
+         . " --limitGenomeGenerateRAM 40419136213 ";
+         
+     if ($gtf_file) {


=====================================
debian/patches/series
=====================================
@@ -1,3 +1,4 @@
+STAR_genomeSAindexNbases
 butterfly
 jellyfish-path
 update-paths
@@ -18,3 +19,4 @@ submake
 skip_blat
 fix-gcc-10.patch
 bamsifter_build
+skip_DTU_STAR_test


=====================================
debian/patches/skip_DTU_STAR_test
=====================================
@@ -0,0 +1,12 @@
+Author: Michael R. Crusoe <crusoe at debian.org>
+Description: Skip the STAR based DTU tests for now
+Forwarded: not-needed
+--- trinityrnaseq.orig/trinity_ext_sample_data/test_DTU/Makefile
++++ trinityrnaseq/trinity_ext_sample_data/test_DTU/Makefile
+@@ -1,5 +1,5 @@
+ test:
+-	./runMe.sh STAR
++	#./runMe.sh STAR
+ 	./runMe.sh HISAT2
+ 
+ clean:



View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/c450962e5f0a2c6200d46bfbb8e0bf1b8a796346...56b1eb8ab745ac57b084cc8e8772e68afccf912a

-- 
View it on GitLab: https://salsa.debian.org/med-team/trinityrnaseq/-/compare/c450962e5f0a2c6200d46bfbb8e0bf1b8a796346...56b1eb8ab745ac57b084cc8e8772e68afccf912a
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