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cluster:73 [2020/06/18 15:22]
hmeij07 [Matlab] 		cluster:73 [2020/06/18 19:03]
hmeij07 [Sequencing Tools]
Line 14: Line 14:
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\ on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\ Some compilations require 7.x and are in /share/apps/CENTOS7 \\
 +
 +====== Sequencing Tools ======
 +
 +  * macs python package (macs2 see below)
 +  * http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
 +  * https://deweylab.github.io/RSEM/
 +  * https://broadinstitute.github.io/picard/
 +  * https://bedtools.readthedocs.io/en/latest/content/installation.html
 +
 +<code>
 +
 +export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
 +export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
 +Successfully installed macs-1.4.3  # note: macs2 Python version must >= 3.6!
 +
 +# or change python version to
 +# ls /share/apps/CENTOS6/python/2.7.9/bin/macs2
 +/share/apps/CENTOS6/python/2.7.9/bin/macs2
 +
 +
 +export PATH="/share/apps/CENTOS6/sequencingtools/bowtie2-2.4.1-linux-x86_64:$PATH"
 +
 +export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib64:/share/apps/CENTOS6/gcc/4.8.4/lib:$LD_LIBRARY_PATH
 +
 +which gcc: /share/apps/CENTOS6/gcc/4.8.4/bin/gcc
 +which python: /share/apps/CENTOS6/miniconda2/bin/python
 +which perl: /share/apps/CENTOS6/miniconda2/bin/perl
 +
 +export PATH=/share/apps/CENTOS6/R/3.6.1b/bin:$PATH
 +export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/3.6.1b/lib64:$LD_LIBRARY_PATH
 +export PATH=/home/apps/CENTOS6/R/packages/bin:$PATH
 +export LD_LIBRARY_PATH=/home/apps/CENTOS6/R/packages/lib:$LD_LIBRARY_PATH
 +which R: /share/apps/CENTOS6/R/3.6.1b/bin/R
 +ldd /home/apps/CENTOS6/R/3.6.1b/lib64/R/bin/exec/R
 +
 +java --version: java 12.0.2 2019-07-16 # /share/apps/java/latest -> jdk-12.0.2
 +java -jar /share/apps/CENTOS6/sequencingtools/picard-2.23.0/picard.jar -h
 +USAGE: PicardCommandLine <program name> [-h]
 +
 +export PATH=/share/apps/CENTOS6/sequencingtools/bedtools-2.29.2/bin:$PATH
 +bedtools --version: bedtools v2.29.2
 +
 +</code>
  
 ====== Deep Learning Software Stack ====== ====== Deep Learning Software Stack ======
cluster/73.txt ยท Last modified: 2024/05/15 12:58 by hmeij07

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