Differences

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--- samtools-software [2016/03/29 12:30] – joguya
+++ samtools-software [2021/09/05 10:32] – aorth
@@ 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: 1.13
-  * Updated: March, 2016
   * Added: February, 2015
-  * Link: http://www.htslib.org/
+  * Updated: September, 2021
+  * Link: http://www.htslib.org
 ===== Usage =====
@@ Line 12: / Line 12: @@
 <code>$ module avail samtools</code>
-Load a particular version of samtools:
+Load a particular version of samtools into your environment and run it:
-<code>$ module load samtools/1.3</code>
+<code>$ module load samtools/1.13
+$ samtools</code>
 ===== Installation =====
 Notes from the sysadmin during installation:
-<code>$ git clone git@github.com:samtools/htslib.git
+<code>$ cd /tmp
-$ git clone git@github.com:samtools/samtools.git
+$ wget https://github.com/samtools/samtools/releases/download/1.13/samtools-1.13.tar.bz2
-$ cd samtools
+$ tar xf samtools-1.13.tar.bz2
-$ git checkout 1.2
+$ cd samtools-1.13
-$ sudo mkdir -p /export/apps/samtools/1.2/
+# install a newer compiler from Red Hat software collections
-$ sudo chown joguya:joguya /export/apps/samtools/1.2/
+$ sudo yum install devtoolset-7-gcc devtoolset-7-gcc-gfortran devtoolset-7-libquadmath-devel devtoolset-7-gcc-c++
+$ scl enable devtoolset-7 bash
+$ ./configure --enable-plugins --enable-libcurl --prefix=/export/apps/samtools/1.13 --with-htslib=/export/apps/htslib/1.13
 $ make
-$ make prefix=/export/apps/samtools/1.2/ install
+$ sudo mkdir -p /export/apps/samtools/1.13
-$ sudo chown -R root:root /export/apps/samtools/1.2/</code>
+$ 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.