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--- cluster:73 [2021/08/19 13:01]
hmeij07 [Kallisto & Trinity & FastQC]
+++ cluster:73 [2021/08/30 18:07]
hmeij07 [Paleogenomics Tools]
@@ Line 510: / Line 510: @@
   * centos7 R v 3.6.0
   * use your HPC username and credentials
+<code>
+# native OS installation for rstudio
+/bin/R
+</code>
 ====== DMTCP =====
@@ Line 634: / Line 641: @@
 </code>
-  * https://github.com/ncbi/sra-tools/
+  * **sratools** https://github.com/ncbi/sra-tools/
   * The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
   * requires centos7 (glibc) so queues mwgpu, amber128, exx96
@@ Line 643: / Line 650: @@
 </code>
+  * **adapterremoval** https://adapterremoval.readthedocs.io/en/latest/index.html
+  * **bwa** https://github.com/lh3/bwa
+  * **bowtie2** http://bowtie-bio.sourceforge.net/bowtie2/index.shtml
+These are all part of Miniconda3 (centos7), to setup the environment consult
+  * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:73#miniconda3
+    * queues: mwgpu, amber128, exx96, debug server greentail52
+They are also available via Miniconda2 (centos6), consult
+  * https://dokuwiki.wesleyan.edu/doku.php?id=cluster:73#miniconda2
+    * queues: hp12, mw256fd, tinymem, debug server swallowtail
+<code>
+[hmeij@greentail52 ~]$ conda list | egrep "adapterremoval|bwa|bowtie"
+adapterremoval            2.3.2                hb7ba0dd_0    bioconda
+bowtie2                   2.2.5            py38hed8969a_7    bioconda
+bwa                       0.7.17               hed695b0_7    bioconda
+</code>
@@ Line 964: / Line 995: @@
   * location: /share/apps/FastQC/0.11.8
   * https://www.bioinformatics.babraham.ac.uk/projects/fastqc/
-  * biolab (jcoolon, tearley)
+  * requires centos6, may not run on centos7
+    * queues: hp12, tinymem, mw256fd mw128
+    * debug server swallowtail
+  * biolab (coolonlab, tearley)

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