Differences

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--- samtools-software [2016/03/29 12:30] – joguya
+++ samtools-software [2017/02/05 11:38] – joguya
@@ Line 2: / Line 2: @@
 samtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
-  * Latest Version: 1.3
+  * Latest Version: 1.3.1
-  * Updated: March, 2016
+  * Updated: February, 2017
   * Added: February, 2015
   * Link: http://www.htslib.org/
@@ Line 14: / Line 14: @@
 Load a particular version of samtools:
-<code>$ module load samtools/1.3</code>
+<code>$ module load samtools/1.3.1</code>
 ===== Installation =====
 Notes from the sysadmin during installation:
-<code>$ git clone git@github.com:samtools/htslib.git
+<code>
-$ git clone git@github.com:samtools/samtools.git
+$ cd /tmp
-$ cd samtools
+$ wget -qO- "https://github.com/samtools/samtools/releases/download/1.3.1/samtools-1.3.1.tar.bz2" | tar xjv
-$ git checkout 1.2
+$ cd samtools-1.3.1/
-$ sudo mkdir -p /export/apps/samtools/1.2/
+$ scl enable devtoolset-2 bash
-$ sudo chown joguya:joguya /export/apps/samtools/1.2/
+$ sudo mkdir /export/apps/samtools/1.3.1
-$ make
+$ sudo chown -R joguya:joguya /export/apps/samtools/1.3.1
-$ make prefix=/export/apps/samtools/1.2/ install
+$ ./configure --enable-plugins --enable-libcurl --with-plugin-path=$PWD/htslib-1.3.1 --prefix=/export/apps/samtools/1.3.1
-$ sudo chown -R root:root /export/apps/samtools/1.2/</code>
+$ make all install-htslib
+$ make install install-htslib
+$ sudo chown -R root:root /export/apps/samtools/1.3.1
+</code>