modified: cre.bcbio.upgrade.sh

	new file:   cre.bcbio.upgrade.star.sh

cre.bcbio.upgrade.sh

@@ -50,7 +50,7 @@
 #########################################################################
 . /hpf/largeprojects/ccmbio/naumenko/tools/bcbio_testing/.test_profile
 which bcbio_nextgen.py
-bcbio_nextgen.py upgrade -u skip --genomes GRCh37 --aligners star --cores 20
+bcbio_nextgen.py upgrade -u skip --genomes GRCh37 --aligners star --cores 10
 #--aligners hisat2 --aligners rtg
 #########################################################################
 # upgrades gemini, cadd, rnaseq if they were installed before, for all references

cre.bcbio.upgrade.star.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+#PBS -l walltime=23:00:00,nodes=1:ppn=10
+#PBS -joe .
+#PBS -d .
+#PBS -l vmem=31g,mem=31g
+
+. /hpf/largeprojects/ccmbio/naumenko/tools/bcbio_testing/.test_profile
+which bcbio_nextgen.py
+
+hostname
+
+# sometimes cannot upgrade STAR on data nodes - memory is low, or cannot take much CPUs
+export PATH=/hpf/largeprojects/ccmbio/naumenko/tools/bcbio_testing/bin:$PATH && STAR \
+--genomeDir /hpf/largeprojects/ccmbio/naumenko/tools/bcbio_testing/genomes/Hsapiens/GRCh37/star \
+--genomeFastaFiles /hpf/largeprojects/ccmbio/naumenko/tools/bcbio_testing/genomes/Hsapiens/GRCh37/seq/GRCh37.fa \
+--runThreadN 10 --limitGenomeGenerateRAM 30000000000 --genomeChrBinNbits 14 --runMode genomeGenerate --genomeSAindexNbases 14
+
+