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--- cluster:73 [2020/06/18 17:43]
hmeij07 [Sequencing Tools]
+++ cluster:73 [2020/06/18 19:03]
hmeij07 [Sequencing Tools]
@@ Line 16: / Line 16: @@
 ====== 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>
@@ Line 21: / Line 27: @@
 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:$PATH"
@@ Line 37: / Line 50: @@
 ldd /home/apps/CENTOS6/R/3.6.1b/lib64/R/bin/exec/R
+java --version: java 12.0.2 2019-07-16 # /share/apps/java/latest -> jdk-12.0.2
+java -jar /share/apps/CENTOS6/sequencingtools/picard-2.23.0/picard.jar -h
+USAGE: PicardCommandLine <program name> [-h]
+export PATH=/share/apps/CENTOS6/sequencingtools/bedtools-2.29.2/bin:$PATH
+bedtools --version: bedtools v2.29.2
 </code>

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