Differences

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--- samtools-software [2015/02/12 11:22] – created joguya
+++ samtools-software [2021/09/05 10:32] – aorth
@@ Line 1: / Line 1: @@
 ====== samtools ======
-  * samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
+samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
-==== v1.2 ====
+  * Latest Version: 1.13
-  * Version: 1.2
   * Added: February, 2015
-  * Link: http://samtools.sourceforge.net/
+  * Updated: September, 2021
+  * Link: http://www.htslib.org
-=== Usage ===
+===== Usage =====
-  * Show all available versions of samtools<code>module avail samtools</code>
+Show all available versions of samtools:
-  * Load samtools module: <code>module load samtools/1.2</code>
-=== Installation ===
+<code>$ module avail samtools</code>
-  * clone samtools repo & compile it<code>git clone git@github.com:samtools/htslib.git
-git clone git@github.com:samtools/samtools.git
-cd samtools
-git checkout 1.2
-sudo mkdir -p /export/apps/samtools/1.2/
-sudo chown joguya:joguya /export/apps/samtools/1.2/
-make
-make prefix=/export/apps/samtools/1.2/ install
-sudo chown -R root:root /export/apps/samtools/1.2/</code>
-  * samtools module file<code>#%Module1.0
-#####################################################################
-##
-## samtools Modulefile
-## by James Oguya <j.oguya@cgiar.org>
-## February, 2015
-##
-set appname         samtools
+Load a particular version of samtools into your environment and run it:
-set version         1.2
-set prefix          /export/apps/${appname}/${version}
-set exec_prefix     ${prefix}/bin
-set datarootdir     ${prefix}/share
-set url "http://samtools.sourceforge.net"
-set msg "This module adds samtools v$version to various paths\n\nsamtools Official Site: $url\n"
-proc ModulesHelp { } {
+<code>$ module load samtools/1.13
-    puts stderr "$msg"
+$ samtools</code>
-}
-module-whatis   "$msg"
+===== Installation =====
+Notes from the sysadmin during installation:
-conflict        samtools
+<code>$ cd /tmp
+$ wget https://github.com/samtools/samtools/releases/download/1.13/samtools-1.13.tar.bz2
-prepend-path    PATH        ${exec_prefix}
+$ tar xf samtools-1.13.tar.bz2
-prepend-path    MANPATH     ${datarootdir}/man
+$ cd samtools-1.13
-</code>
+# install a newer compiler from Red Hat software collections
+$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
-  * deploy the new module using ansible<code>ansible-playbook site.yml -u provisioning -K -s --limit=compute --tags=modules</code>
+$ scl enable devtoolset-7 bash
+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.13 --with-htslib=/export/apps/htslib/1.13
+$ make
+$ sudo mkdir -p /export/apps/samtools/1.13
+$ sudo chown aorth /export/apps/samtools/1.13
+$ make install
+$ sudo chown -R root:root /export/apps/samtools/1.13</code>
+This links against htslib/1.13, which is installed as a module.