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cluster:73 [2020/06/18 17:27]
hmeij07 [Sequencing Tools] 		cluster:73 [2020/06/18 18:57]
hmeij07 [Sequencing Tools]
Line 16: Line 16:
  
 ====== Sequencing Tools ====== ====== Sequencing Tools ======
 +
 +  * macs python package
 +  * 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> <code>
Line 21: Line 27:
 export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH" export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
 export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH" export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
 +Successfully installed macs-1.4.3  # note: macs2 Python version must >= 3.6!
 +
 export PATH="/share/apps/CENTOS6/sequencingtools/bowtie2-2.4.1-linux-x86_64:$PATH" export PATH="/share/apps/CENTOS6/sequencingtools/bowtie2-2.4.1-linux-x86_64:$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 python: /share/apps/CENTOS6/miniconda2/bin/python
-which g++: /usr/bin/g++ 
 which perl: /share/apps/CENTOS6/miniconda2/bin/perl which perl: /share/apps/CENTOS6/miniconda2/bin/perl
  
 export PATH=/share/apps/CENTOS6/R/3.6.1b/bin:$PATH export PATH=/share/apps/CENTOS6/R/3.6.1b/bin:$PATH
 export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/3.6.1b/lib64:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/3.6.1b/lib64:$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 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> </code>
cluster/73.txt ยท Last modified: 2024/05/15 12:58 by hmeij07

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