# HG changeset patch
# User crs4
# Date 1415298015 18000
# Node ID 1fea05cdc1a1b1bf73128b85cc33739358793875
# Parent  6adb6e16b00fb12966f1e012e1612d356ca021d4
Update Orione citation. Upgrade Mosaik dependency to v. 2.2.28 (2.2.30 is buggy, see https://github.com/wanpinglee/MOSAIK/issues/11 ). Use 2.1.78 neural networks. Add package_zlib_1_2_8 and package_samtools_0_1_19 dependencies. Add <citations>.

diff -r 6adb6e16b00f -r 1fea05cdc1a1 mosaik2.xml
--- a/mosaik2.xml	Wed Apr 02 12:32:52 2014 -0400
+++ b/mosaik2.xml	Thu Nov 06 13:20:15 2014 -0500
@@ -1,8 +1,8 @@
 <?xml version="1.0"?>
-<tool id="mosaik2" name="Map with MOSAIK v. 2" version="2.0.0">
+<tool id="mosaik2" name="Map with MOSAIK v. 2" version="2.2.28.0">
   <description/>
   <requirements>
-    <requirement type="package" version="2.2.26">mosaik</requirement>
+    <requirement type="package" version="2.2.28">mosaik</requirement>
     <requirement type="package" version="0.1.19">samtools</requirement>
   </requirements>
   <version_command>MosaikJump | sed -e 's/\x1b\[[[:digit:]]\{1,2\}\(;[[:digit:]]\{1,2\}\)\{0,1\}m//g' | sed -n 's/MosaikJump \([[:digit:].]\{1,\}\).*/\1/p'</version_command>
@@ -23,7 +23,7 @@
       #set $ls_string = '-ls %s' % $paired.ls
     #end if
     -st $st -out mosaik_reads_file;
-    MosaikAligner -p \${GALAXY_SLOTS:-4} -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file -annpe \$MOSAIK_NETWORK_DIR/2.1.26.pe.100.0065.ann -annse \$MOSAIK_NETWORK_DIR/2.1.26.se.100.005.ann $ls_string
+    MosaikAligner -p \${GALAXY_SLOTS:-4} -ia mosaik_ref_file -in mosaik_reads_file -out mosaik_aligned_file -annpe \$MOSAIK_NETWORK_DIR/2.1.78.pe.ann -annse \$MOSAIK_NETWORK_DIR/2.1.78.se.ann $ls_string
     #if str($mm)
       -mm $mm
     #end if
@@ -36,7 +36,7 @@
     #if str($mhp)
       -mhp $mhp
     #end if
-    -hs 15;
+    -hs 15 &amp;&amp;
     #if str($outFormat) == 'bam'
       samtools sort -o mosaik_aligned_file.bam out_prefix &gt; $output
     #else
@@ -141,15 +141,22 @@
 .. _CRS4 Srl.: http://www.crs4.it/
 .. _Academic Free License v. 3.0: http://opensource.org/licenses/AFL-3.0
 
-If you use this tool in Galaxy, please cite |Cuccuru2014|_.
-
-.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics*, accepted
-.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/early/2014/03/10/bioinformatics.btu135
-
-This tool uses `MOSAIK`_, which is licensed separately. Please cite |Lee2014|_.
+You can use this tool only if you agree to the license terms of: `MOSAIK`_.
 
 .. _MOSAIK: https://code.google.com/p/mosaik-aligner/
+
+If you use this tool, please cite:
+
+- |Cuccuru2014|_
+- |Lee2014|_.
+
+.. |Cuccuru2014| replace:: Cuccuru, G., Orsini, M., Pinna, A., Sbardellati, A., Soranzo, N., Travaglione, A., Uva, P., Zanetti, G., Fotia, G. (2014) Orione, a web-based framework for NGS analysis in microbiology. *Bioinformatics* 30(13), 1928-1929
+.. _Cuccuru2014: http://bioinformatics.oxfordjournals.org/content/30/13/1928
 .. |Lee2014| replace:: Lee, W.-P., *et al.* (2014) MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping. *PLoS ONE* 9(3), e90581
 .. _Lee2014: http://www.plosone.org/article/info:doi/10.1371/journal.pone.0090581
   </help>
+  <citations>
+    <citation type="doi">10.1093/bioinformatics/btu135</citation>
+    <citation type="doi">10.1371/journal.pone.0090581</citation>
+  </citations>
 </tool>
diff -r 6adb6e16b00f -r 1fea05cdc1a1 readme.rst
--- a/readme.rst	Wed Apr 02 12:32:52 2014 -0400
+++ b/readme.rst	Thu Nov 06 13:20:15 2014 -0500
@@ -19,6 +19,7 @@
 Version history
 ---------------
 
+- Release 1: Update Orione citation. Upgrade Mosaik dependency to v. 2.2.28 (2.2.30 is buggy, see https://github.com/wanpinglee/MOSAIK/issues/11 ). Use 2.1.78 neural networks. Add package_zlib_1_2_8 and package_samtools_0_1_19 dependencies. Add <citations>.
 - Release 0: Initial release in the Tool Shed.
 
 Development
diff -r 6adb6e16b00f -r 1fea05cdc1a1 tool_dependencies.xml
--- a/tool_dependencies.xml	Wed Apr 02 12:32:52 2014 -0400
+++ b/tool_dependencies.xml	Thu Nov 06 13:20:15 2014 -0500
@@ -1,11 +1,20 @@
 <?xml version="1.0"?>
 <tool_dependency>
-  <package name="mosaik" version="2.2.26">
+  <package name="zlib" version="1.2.8">
+    <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
+  <package name="mosaik" version="2.2.28">
     <install version="1.0">
       <actions>
         <action type="shell_command">git clone https://github.com/wanpinglee/MOSAIK.git mosaik</action>
-        <action type="shell_command">git reset --hard e04c806bb1410cf1dbd1534991c46d696aec6723</action>
+        <action type="shell_command">git reset --hard 24cf066048228a729c79f1de06b403ad8b0bc920</action>
         <action type="shell_command">sed -i 's/ -static//g' src/includes/linux.inc</action>
+        <!-- populate the environment variables from the dependent repos -->
+        <action type="set_environment_for_install">
+          <repository changeset_revision="63a4a902cda2" name="package_zlib_1_2_8" owner="iuc" toolshed="https://toolshed.g2.bx.psu.edu">
+            <package name="zlib" version="1.2.8" />
+          </repository>
+        </action>
         <action type="shell_command">make -C src/</action>
         <action type="move_directory_files">
           <source_directory>bin</source_directory>
@@ -16,15 +25,15 @@
           <destination_directory>$INSTALL_DIR/networkFile</destination_directory>
         </action>
         <action type="set_environment">
-          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+          <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
         </action>
         <action type="set_environment">
-          <environment_variable name="MOSAIK_NETWORK_DIR" action="set_to">$INSTALL_DIR/networkFile</environment_variable>
+          <environment_variable action="set_to" name="MOSAIK_NETWORK_DIR">$INSTALL_DIR/networkFile</environment_variable>
         </action>
       </actions>
     </install>
   </package>
-<!--  <package name="samtools" version="0.1.19">
-    <repository name="package_samtools_0_1_19" owner="devteam" />
-  </package>-->
+  <package name="samtools" version="0.1.19">
+    <repository changeset_revision="1ef76f8d8e52" name="package_samtools_0_1_19" owner="devteam" toolshed="https://toolshed.g2.bx.psu.edu" />
+  </package>
 </tool_dependency>