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cluster:73 [2019/10/02 14:31]
hmeij07 [OpenStructure] 		cluster:73 [2020/01/14 14:57]
hmeij07 [Paleogenomics Tools]
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 The list of software was primarily compiled under RHEL5.1 but more recent compilation are done on host sharptail under RHEL5.5. Newer compilations are done with CentOS 6.5 (since summer 2013) on either swallowtail or node n33. The list of software was primarily compiled under RHEL5.1 but more recent compilation are done on host sharptail under RHEL5.5. Newer compilations are done with CentOS 6.5 (since summer 2013) on either swallowtail or node n33.
 +
 +====== Paleogenomics Tools ======
 +
 +Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories:
 +
 +  * http://www.htslib.org/download/
 +  * Samtools: Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format
 +  * BCFtools:Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
 +  * HTSlib: A C library for reading/writing high-throughput sequencing data 
 +
 +<code>
 +
 +# add to environment
 +export PATH=/share/apps/CENTOS6/samtools/1.10/bin:$PATH
 +export PATH=/share/apps/CENTOS6/bcftools/1.10.2/bin:$PATH
 +export PATH=/share/apps/CENTOS6/htslib/1.10.2/bin:$PATH
 +
 +</code>
 +
 +   * https://github.com/ANGSD/angsd
 +   * Program for analysing NGS data
 +
 +<code>
 +
 +# does not seem to work against htslib version above...
 +export  HTSSRC=/share/apps/CENTOS6/ANGSD/htslib
 +export PATH=/share/apps/CENTOS6/ANGSD/angsd:$PATH
 +
 +</code>
  
 ====== CD-HIT ====== ====== CD-HIT ======
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   export PATH=/share/apps/CENTOS6/R/packages/bin:$PATH   export PATH=/share/apps/CENTOS6/R/packages/bin:$PATH
   export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/packages/lib:$LD_LIBRARY_PATH   export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/packages/lib:$LD_LIBRARY_PATH
-  export PATH=/share/apps/CENTOS6/R/3.6.1/bin:$PATH +  export PATH=/share/apps/CENTOS6/R/3.6.1b/bin:$PATH 
-  export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/3.6.1/lib64:$LD_LIBRARY_PATH+  export LD_LIBRARY_PATH=/share/apps/CENTOS6/R/3.6.1b/lib64:$LD_LIBRARY_PATH
   export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH   export PATH=/share/apps/CENTOS6/gcc/4.8.4/bin:$PATH
   export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib64:/share/apps/CENTOS6/gcc/4.8.4/lib:$LD_LIBRARY_PATH   export LD_LIBRARY_PATH=/share/apps/CENTOS6/gcc/4.8.4/lib64:/share/apps/CENTOS6/gcc/4.8.4/lib:$LD_LIBRARY_PATH
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   * Python 2.7.15   * Python 2.7.15
     * compile with enable-share     * compile with enable-share
-    * numpy and scipy packages+    * numpy and scipy packages, and 
 +    * Successfully installed Send2Trash-1.5.0 backports-abc-0.5 futures-3.3.0 ipaddress-1.0.22  
 +    * ipykernel-4.10.1 jupyter-client-5.3.4 jupyterlab-0.33.12 jupyterlab-launcher-0.11.2  
 +    * notebook-5.7.8 prometheus-client-0.7.1 python-dateutil-2.8.0 singledispatch-3.4.0.3  
 +    * subprocess32-3.5.4 terminado-0.8.2 tornado-5.1.1 
  
 <code> <code>
cluster/73.txt · Last modified: 2024/05/15 12:58 by hmeij07

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