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cluster:73 [2021/08/19 12:22]
hmeij07 [Sequencing Tools #4]
cluster:73 [2021/08/30 18:07]
hmeij07 [Paleogenomics Tools]
Line 18: Line 18:
 on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\ on either cottontail2 or node n33 located at /share/apps/CENTOS6 \\
 Some compilations require 7.x and are in /share/apps/CENTOS7 \\ Some compilations require 7.x and are in /share/apps/CENTOS7 \\
 +
 +====== 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 ====== ====== Sequencing Tools #4 ======
 +
 +Added to miniconda3, see section "Miniconda3"
 +
 +  * Requires centos7 so queues mwgpu, amber128, exx96
 +    * debug server greentail52
 +    * PREFIX=/share/apps/CENTOS7/miniconda3
 +    * python 3.9
 +  * jcoolon lab
 +    
  
 <code> <code>
Line 35: Line 52:
     bedtools-2.30.0            |       hc088bd4_0        14.0 MB  bioconda     bedtools-2.30.0            |       hc088bd4_0        14.0 MB  bioconda
  
 +# cufflinks requires centos 6, weird, so also added to miniconda2,  
 +# see section "Kallisto & Trinity & FastQC"
  
 </code> </code>
Line 492: Line 510:
   * centos7 R v 3.6.0   * centos7 R v 3.6.0
   * use your HPC username and credentials   * use your HPC username and credentials
 +
 +<code>
 +
 +# native OS installation for rstudio
 +/bin/R
 +
 +</code>
  
 ====== DMTCP ===== ====== DMTCP =====
Line 616: Line 641:
 </code> </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.   * 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   * requires centos7 (glibc) so queues mwgpu, amber128, exx96
Line 625: Line 650:
  
 </code> </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 946: Line 995:
   * location: /share/apps/FastQC/0.11.8   * location: /share/apps/FastQC/0.11.8
   * https://www.bioinformatics.babraham.ac.uk/projects/fastqc/   * 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 956: Line 1008:
 <code> <code>
  
 +# env
 export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH" export PATH="/share/apps/CENTOS6/miniconda2/bin:$PATH"
 export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH" export LD_LIBRARY_PATH="/share/apps/CENTOS6/miniconda2/lib:$LD_LIBRARY_PATH"
Line 969: Line 1022:
   hdf5               conda-forge/linux-64::hdf5-1.10.3-hba1933b_1001   hdf5               conda-forge/linux-64::hdf5-1.10.3-hba1933b_1001
   kallisto           bioconda/linux-64::kallisto-0.45.0-hdcc98e5_0   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> </code>
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07