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--- cluster:73 [2019/10/02 17:42]
hmeij07 [R & R/parallel]
+++ cluster:73 [2020/01/14 14:40]
hmeij07 [Paleogenomics Tools]
@@ Line 11: / Line 11: @@
 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:
+  * 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>
 ====== CD-HIT ======
@@ Line 2377: / Line 2394: @@
   * Python 2.7.15
     * 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>

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