15458dfbac
This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded.
33 lines
1 KiB
Bash
33 lines
1 KiB
Bash
--- calcmem.sh.orig 2021-04-13 14:05:28 UTC
|
|
+++ calcmem.sh
|
|
@@ -72,30 +72,6 @@ function setEnvironment(){
|
|
if [[ $SHIFTER_RUNTIME == 1 ]]; then
|
|
#Ignore NERSC_HOST
|
|
shifter=1
|
|
- elif [ -v "$EC2_HOME" ]; then
|
|
- #Let's assume this is the AWS taxonomy server...
|
|
- PATH=/test1/binaries/bgzip:$PATH
|
|
- PATH=/test1/binaries/lbzip2/bin:$PATH
|
|
- PATH=/test1/binaries/sambamba:$PATH
|
|
- #PATH=/test1/binaries/java/jdk-11.0.2/bin:$PATH
|
|
- PATH=/test1/binaries/pigz2/pigz-2.4:$PATH
|
|
- elif [ -z "$NERSC_HOST" ]; then
|
|
- #Not NERSC; do nothing
|
|
- :
|
|
- else
|
|
- PATH=/global/projectb/sandbox/gaag/bbtools/bgzip:$PATH
|
|
- PATH=/global/projectb/sandbox/gaag/bbtools/lbzip2/bin:$PATH
|
|
- PATH=/global/projectb/sandbox/gaag/bbtools/sambamba:$PATH
|
|
- PATH=/global/projectb/sandbox/gaag/bbtools/java/jdk-11.0.2/bin:$PATH
|
|
- PATH=/global/projectb/sandbox/gaag/bbtools/pigz2/pigz-2.4:$PATH
|
|
-
|
|
- if [[ $NERSC_HOST == cori ]]; then
|
|
-
|
|
- #module unload PrgEnv-intel
|
|
- #module load PrgEnv-gnu/7.1
|
|
- PATH=/global/projectb/sandbox/gaag/bbtools/samtools_cori/bin:$PATH
|
|
- :
|
|
- fi
|
|
fi
|
|
}
|
|
|