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--- cluster:73 [2021/08/19 12:36]
hmeij07 [Sequencing Tools #4]
+++ cluster:73 [2021/10/15 14:09]
hmeij07 [Hoomd]
@@ Line 18: / Line 18: @@
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\
+====== Hoomd ======
+HOOMD-blue is a Python package that runs simulations of particle systems on CPUs and GPUs.
+  * https://hoomd-blue.readthedocs.io/en/latest/index.html
+  * requires both minconda3 (centos7) **and** cuda-10.2 (so queue exx96 only)
+  * starrlab
+Set up env for miniconda and cuda
+<code>
+ export CUDAHOME=/usr/local/cuda-10.2
+ export PATH=/usr/local/cuda-10.2/bin:$PATH
+ export LD_LIBRARY_PATH=/usr/local/cuda-10.2/lib:$LD_LIBRARY_PATH
+ export LD_LIBRARY_PATH=/usr/local/cuda-10.2/lib64:$LD_LIBRARY_PATH
+ source /share/apps/CENTOS7/amber/miniconda3/etc/profile.d/conda.sh
+ export PATH=/share/apps/CENTOS7/amber/miniconda3/bin:$PATH
+ export LD_LIBRARY_PATH=/share/apps/CENTOS7/amber/miniconda3/lib:$LD_LIBRARY_PATH
+ which mpirun python conda
+ which nvcc
+# installation (not sure how this works, does the * not get expanded in shell?)
+# seems to have worked forcing gpu package install on greentail52
+ conda install -c conda-forge hoomd=*=*gpu*
+$ conda list | egrep -i "cuda|hoomd"
+cudatoolkit               11.0.221             h6bb024c_0
+hoomd                     2.9.4           gpu_py38h02d30ca_1    conda-forge
+</code>
+   * installed/updated were...
+<code>
+    ca-certificates-2021.10.8  |       ha878542_0         139 KB  conda-forge
+    certifi-2021.10.8          |   py38h578d9bd_0         145 KB  conda-forge
+    conda-4.10.3               |   py38h578d9bd_2         3.0 MB  conda-forge
+    cudatoolkit-11.0.221       |       h6bb024c_0       622.9 MB
+    hoomd-2.9.4                |gpu_py38h02d30ca_1        46.2 MB  conda-forge
+    openssl-1.1.1h             |       h516909a_0         2.1 MB  conda-forge
+    tbb-2020.2                 |       hc9558a2_0         1.4 MB  conda-forge
+</code>
+===== Miniconda2 =====
+  * miniconda2 (python 2.7) is hiding in section
+  * "Kallisto & Trinity & FastQC"
+    * some packages require centos 6 (like cufflinks)
+  * many packages are also available in miniconda3 section
+    * requires centos 7 (python 3.9)
 ====== Sequencing Tools #4 ======
@@ Line 502: / Line 559: @@
   * centos7 R v 3.6.0
   * use your HPC username and credentials
+<code>
+# native OS installation for rstudio
+/bin/R
+</code>
 ====== DMTCP =====
@@ Line 626: / Line 690: @@
 </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 635: / Line 699: @@
 </code>
+  * **adapterremoval** https://github.com/MikkelSchubert/adapterremoval
+  * **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 956: / Line 1044: @@
   * 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 966: / Line 1057: @@
 <code>
+# env
 export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
 export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
@@ Line 979: / Line 1071: @@
   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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