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--- cluster:73 [2020/06/18 15:27]
hmeij07 [Deep Learning Software Stack]
+++ cluster:73 [2020/06/18 19:03]
hmeij07 [Sequencing Tools]
@@ Line 15: / Line 15: @@
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\
-====== Miniconda2 ======
+====== 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>
-Installing collected packages: MarkupSafe, jinja2, markdown, click, python-engineio, python-socketio, Werkzeug, itsdangerous, flask, flask-socketio, greenlet, dnspython, monotonic, eventlet, future, msgpack-python, bowtie
-Successfully installed MarkupSafe-1.1.1 Werkzeug-1.0.1 bowtie-0.8.1 click-7.1.2 dnspython-1.16.0 eventlet-0.25.2 flask-1.1.2 flask-socketio-4.3.0 future-0.18.2 greenlet-0.4.16 itsdangerous-1.1.0 jinja2-2.11.2 markdown-3.1.1 monotonic-1.5 msgpack-python-0.5.6 python-engineio-3.13.0 python-socketio-4.6.0
+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>

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