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--- cluster:73 [2021/08/19 12:58]
hmeij07 [Kallisto & Trinity & FastQC]
+++ cluster:73 [2021/08/30 17:46]
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, to setup the environment consult
+<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 987: @@
   * 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)
@@ Line 974: / Line 1000: @@
 <code>
- --- //[[hmeij@wesleyan.edu|Henk]] 2021/08/19 08:55//
+# env
-\\
-Added packages below for Prof Coolon's lab (skalra)
-<code>
-conda list | egrep -i "samtools|bowtie2|bedtools|cufflinks"
-bedtools                  2.30.0               h7d7f7ad_1    bioconda
-bowtie2                   2.3.5.1          py27he513fc3_0    bioconda
-cufflinks                 2.2.1                    py27_2    bioconda
-samtools                  1.13                 h8c37831_0    bioconda
-</code>
 export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
 export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
@@ Line 1001: / Line 1014: @@
   hdf5               conda-forge/linux-64::hdf5-1.10.3-hba1933b_1001
   kallisto           bioconda/linux-64::kallisto-0.45.0-hdcc98e5_0
+# --- //[[hmeij@wesleyan.edu|Henk]] 2021/08/19 08:55//
+# Added packages below for Prof Coolon's lab (skalra)
+conda list | egrep -i "samtools|bowtie2|bedtools|cufflinks"
+bedtools                  2.30.0               h7d7f7ad_1    bioconda
+bowtie2                   2.3.5.1          py27he513fc3_0    bioconda
+cufflinks                 2.2.1                    py27_2    bioconda
+samtools                  1.13                 h8c37831_0
 </code>

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