Differences

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--- pandaseq-software [2014/10/07 13:40] – created joguya
+++ pandaseq-software [2014/12/08 09:27] (current) – [Installation Notes] joguya
@@ Line 1: / Line 1: @@
 ====== Pandaseq ======
-Pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
+Pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
-===== Information =====
+===== Pandaseq 2.7 =====
+Information
   * Version: 2.7
   * Added: October, 2014
@@ Line 9: / Line 10: @@
+==== Usage ====
-===== Usage =====
 === Show available version ===
   * <code>module avail pandaseq</code>
 === Show manpages ===
-  * Load pandaseq module: <code>module load pandaseq/2.7</code>
+  * Load pandaseq module: <code>module load pandaseq/2.7
-  * <code>man pandaseq</code>
+man pandaseq</code>
-===== Installation ======
+==== Installation ====
   * clone repo from [[https://github.com/neufeld/pandaseq.git|github]] <code>cd /home/joguya/src
 git clone https://github.com/neufeld/pandaseq.git
@@ Line 32: / Line 33: @@
 make install </code>
   * change ownership back to root<code>sudo chown -R root:root /export/apps/pandaseq/2.7/</code>
+  * module file for version 2.7<code>
+#%Module1.0#####################################################################
+##
+## pandaseq modulefile
+## By James Oguya <j.oguya@cgiar.org>
+## October, 2014
+##
+module-whatis "pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence."
+# for Tcl script use only
+set     appname         pandaseq
+set     version         2.7
+set     prefix          /export/apps/${appname}/${version}
+set     exec_prefix     ${prefix}/bin
+set     datarootdir     ${prefix}/share
+conflict        pandaseq
+prepend-path    PATH            ${exec_prefix}
+prepend-path    MANPATH         ${datarootdir}/man
+</code>
+  * deploy the new module using ansible<code>ansible-playbook site.yml -u joguya -K -s --limit=compute --tags=module</code>
+  * do a quick module load/unload to perform a quick test<code>module load pandaseq/2.7
+pandaseq -h
+man pandaseq
+</code>
+===== Pandaseq 2.8.1 =====
+Information:
+  * Version: 2.8.1
+  * Added: December, 2014
+  * Link: https://github.com/neufeld/pandaseq/releases/tag/v2.8.1
+changelog:
+  * Add a plugin to display overlaps examined
+  * Add -D flag to add a penalty for shifting primers
+  * Added UPARSE algorithm
+  * Add FastqJoin algorithm
+  * Add FLASH algorithm
+  * Add Sitch algorithm
+  * Fix bug causing spurious "no sequences" with one thread
+  * Issue an error if the command line arguments have UTF-8 characters
+  * Remove min_readqscore since it doesn't work as advertised
+  * Sanity check sequence length after primer stripping
+==== Installation Notes ====
+  * Download pandaseq 2.8.1, create version specific dir in /export/apps/pandaseq/, compile & install it.<code>
+wget https://github.com/neufeld/pandaseq/archive/v2.8.1.tar.gz -O pandaseq-v2.8.1.tar.gz
+tar -xvf pandaseq-v2.8.1.tar.gz
+cd pandaseq-v2.8.1
+sudo mkdir /export/apps/pandaseq/2.8.1/
+sudo chown -R joguya:joguya /export/apps/pandaseq/2.8.1
+./autogen.sh
+./configure --prefix=/export/apps/pandaseq/2.8.1
+make
+make install
+sudo chown -R root:root /export/apps/pandaseq/2.8.1
+</code>
+  * pandaseq/2.8.1 module file:<code>
+#%Module1.0
+#####################################################################
+##
+## Pandaseq Modulefile
+## By James Oguya, j.oguya@cgiar.org
+## December, 2014
+##
+set appname         pandaseq
+set version         2.8.1
+set prefix          /export/apps/${appname}/${version}
+set exec_prefix     ${prefix}/bin
+set url "https://github.com/neufeld/pandaseq/"
+set msg "pandaseq is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.\nPandaseq Official Site: $url\n"
+module-whatis $msg
+proc ModulesHelp { } {
+    puts stderr "$msg"
+}
+conflict        pandaseq
+prepend-path    PATH        ${exec_prefix}
+prepend-path    MANPATH     ${prefix}/share/man
+</code>