Differences

This shows you the differences between two versions of the page.

--- pear-software [2020/04/16 10:51] – aorth
+++ pear-software [2020/04/16 11:14] (current) – aorth
@@ Line 5: / Line 5: @@
 ===== Information =====
-  * Version: git-2c309dc
+  * Version: 0.9.6
   * Added: September, 2016
+  * Updated: April, 2020
   * Link: https://www.h-its.org/software/pear-paired-end-read-merger/
@@ Line 14: / Line 15: @@
 <code>$ module avail pear</code>
-Load pear
+Load one version into your environment and run it:
-<code>$ module load pear</code>
+<code>$ module load pear/0.9.6
+$ pear</code>
+Note: please use the ''-j'' option to control how many CPU threads pear uses. This should match the number of CPUs you requested in your SLURM SBATCH job parameters.
 ===== Installation ======
 Notes from the sysadmin during installation:
 <code>
 $ cd /tmp
-$ git clone https://github.com/xflouris/PEAR.git
+$ wget https://depot.galaxyproject.org/software/pear/pear_0.9.6_src_all.tar.gz
-$ sudo mkdir -p /export/apps/pear/git-2c309dc
+$ tar xf pear_0.9.6_src_all.tar.gz
-$ sudo chown -R joguya:joguya /export/apps/pear/git-2c309dc
+$ cd pear-0.9.6-src
-$ scl enable devtoolset-2 bash
+$ scl enable devtoolset-7 bash
-$ ./autogen.sh
+$ ./configure --prefix=/export/apps/pear/0.9.6
-$ ./configure --disable-zlib --prefix=/export/apps/pear/git-2c309dc
 $ make
+$ sudo mkdir -p /export/apps/pear/0.9.6
+$ sudo chown aorth /export/apps/pear/0.9.6
 $ make install
-$ sudo chown -R root:root /export/apps/pear/git-2c309dc
+$ sudo chown -R root:root /export/apps/pear/0.9.6
 </code>
+Note: I downloaded this from galaxyproject because the upstream site requires academic registration and I never received the confirmation mail to download the software. Also, this is the URL that is used by Conda.