These are chat archives for biom262/biom262-2016

14th
Mar 2016
ericsan119
@ericsan119
Mar 14 2016 05:07
Does anyone know how to install Varscan on TSCC?
mbaughn
@mbaughn
Mar 14 2016 05:08
Module load biotools?
mbaughn
@mbaughn
Mar 14 2016 05:22
Nope, nm… definitely not that
[tscc-login1 ps-yeolab]$ tree -f | grep 'varscan'
│   │   │   ├── ./biom262-2015/biom262_harismendy/class1/varscan.err
│   │   │   ├── ./biom262-2015/biom262_harismendy/class1/varscan.out
│   │   │   └── ./biom262-2015/biom262_harismendy/class1/varscan.sh
│   │   │   └── ./biom262-2015/biom262_harismendy/resources/varscan_dna_copy_rcode.r
│   │   ├── ./biom262-2015/biom262_harismendy/varscan
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CNA.out.copynumber
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/countcommand.txt
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES14.pileup
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1.pileup
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_DNACopy_merged.copynumber
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered_hc_failed.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered_hc_germlineLOH.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered_hc.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered_hc_somatic.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered.indel
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_filtered.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14.indel
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14.snp
│   │   │   ├── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_totalPassed_somatic_coding.table
│   │   │   └── ./biom262-2015/biom262_harismendy/varscan/CPTRES1_vs_CPTRES14_totalPassed_somatic.table
│   │   ├── ./biom262-2015/tools/varscan
│   │   │   ├── ./biom262-2015/tools/varscan/fpfilter.pl
│   │   │   ├── ./biom262-2015/tools/varscan/mergeSegments.pl
│   │   │   └── ./biom262-2015/tools/varscan/VarScan.v2.3.7.jar
│   │   │   └── ./biom262_2016/data/PBSscripts/varscan.sh
│       ├── ./biom262_2016/tools/varscan
│       │   └── ./biom262_2016/tools/varscan/VarScan.v2.3.9.jar
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found it!
java -jar /projects/ps-yeolab/biom262_2016/tools/varscan/VarScan.v2.3.9.jar
at least that is the directory we used in class
ericsan119
@ericsan119
Mar 14 2016 07:10
Thanks~
Yiren Hu
@Charlottehu
Mar 14 2016 07:25
@olgabot just to clarify, for the exam question 1.3) a) , are we going to merge these two files and give a single answer or give separate answers for each file?
Jamison M McCorrison
@bioh4x
Mar 14 2016 15:23
Hi Charlotte, For 1.3, it is intended that you provide answers for each file separately, though I would accept the merged file solution as long as the unix methods are provided!
andersonbrookee
@andersonbrookee
Mar 14 2016 23:00
Any words of advice on this?
Error: Could not create the Java Virtual Machine. Error: A fatal exception has occurred. Program will exit.
Happens when I try to use anything with java, including java -jar, java -version, and java -help
andersonbrookee
@andersonbrookee
Mar 14 2016 23:06
nvm turns out I don't need that to run.
andersonbrookee
@andersonbrookee
Mar 14 2016 23:15
still getting issues trying to run vcffilter though. Keep getting a ton of
Input stream not ready, waiting for 5 seconds...
before it just aborts