# HG changeset patch
# User jmchilton
# Date 1436017092 14400
# Node ID b4f1eee85d8dd6d2d43b5b6744b8a46f550c69d7
# Parent  58eb64dff5b428d5fd98668d1721abe078dcca02
planemo upload

diff -r 58eb64dff5b4 -r b4f1eee85d8d tool_dependencies.xml
--- a/tool_dependencies.xml	Sat Jul 04 09:36:08 2015 -0400
+++ b/tool_dependencies.xml	Sat Jul 04 09:38:12 2015 -0400
@@ -1,72 +1,82 @@
-<?xml version='1.0' encoding='utf-8'?>
+<?xml version="1.0"?>
 <tool_dependency>
-    <package name="blast+" version="2.2.26+">
-        <install version="1.0">
-            <actions_group>
-                <!-- Download the binaries for BLAST+ compatible with 64-bit OSX. -->
-                <actions os="darwin" architecture="x86_64">
-                    <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</action>
-                    <action type="move_directory_files">
-                         <source_directory>bin</source_directory>
-                         <destination_directory>$INSTALL_DIR</destination_directory>
-                     </action>
-                </actions>
-                <!-- Download the binaries for BLAST+ compatible with 32-bit OSX. -->
-                <actions os="darwin" architecture="i386">
-                    <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-universal-macosx.tar.gz</action>
-                    <action type="move_directory_files">
-                        <source_directory>bin</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                <!-- Download the binaries for BLAST+ compatible with 64-bit Linux. -->
-                <actions os="linux" architecture="x86_64">
-                    <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-x64-linux.tar.gz</action>
-                    <action type="move_directory_files">
-                        <source_directory>bin</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i386). -->
-                <actions os="linux" architecture="i386">
-                    <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</action>
-                    <action type="move_directory_files">
-                        <source_directory>bin</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                <!-- Download the binaries for BLAST+ compatible with 32-bit Linux (i686). -->
-                <actions os="linux" architecture="i686">
-                    <action type="download_by_url">ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.2.26/ncbi-blast-2.2.26+-ia32-linux.tar.gz</action>
-                    <action type="move_directory_files">
-                        <source_directory>bin</source_directory>
-                        <destination_directory>$INSTALL_DIR</destination_directory>
-                    </action>
-                </actions>
-                <!-- This actions tag is only processed if none of the above tags resulted in a successful installation. -->
-                <actions>
-                    <action type="shell_command">echo "ERROR: Automated installation on your operating system and CPU architecture combination is not yet supported."</action>
-                    <action type="shell_command">echo "Your machine details (the output from 'uname' and 'arch'):"</action>
-                    <action type="shell_command">uname</action>
-                    <action type="shell_command">arch</action>
-                    <action type="shell_command">echo "Please report this via https://github.com/peterjc/galaxy_blast/issues - thank you!"</action>
-                    <action type="shell_command">false</action>
-                    <!-- The 'false' command will return an error, so Galaxy should treat this as a failed install -->
-                </actions>
-                <!-- The $PATH environment variable is only set if one of the above <actions> tags resulted in a successful installation. -->
-                <action type="set_environment">
-                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR</environment_variable>
-                </action>
-            </actions_group>
-        </install>
+  <package name="samtools" version="0.1.16">
+    <install version="1.0">
+      <actions_group>
+        <actions os="linux" architecture="i386">
+          <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/i386/samtools/samtools-0.1.16-linux-i386.tgz</action>
+          <action type="move_directory_files">
+            <source_directory>.</source_directory>
+            <destination_directory>$INSTALL_DIR</destination_directory>
+          </action>
+        </actions>
+        <actions os="linux" architecture="x86_64">
+          <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-0.1.16-linux-x86_64.tgz</action>
+          <action type="move_directory_files">
+            <source_directory>.</source_directory>
+            <destination_directory>$INSTALL_DIR</destination_directory>
+          </action>
+        </actions>
+        <actions os="darwin" architecture="i386">
+          <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/i386/samtools/samtools-0.1.16-Darwin-i386.tgz</action>
+          <action type="move_directory_files">
+            <source_directory>.</source_directory>
+            <destination_directory>$INSTALL_DIR</destination_directory>
+          </action>
+        </actions>
+        <actions os="darwin" architecture="x86_64">
+          <action type="download_by_url" target_filename="samtools-0.1.16.tgz">http://depot.galaxyproject.org/package/darwin/x86_64/samtools/samtools-0.1.16-Darwin-x86_64.tgz</action>
+          <action type="move_directory_files">
+            <source_directory>.</source_directory>
+            <destination_directory>$INSTALL_DIR</destination_directory>
+          </action>
+        </actions>
+        <actions>
+          <action type="download_by_url">http://depot.galaxyproject.org/package/source/samtools/samtools-0.1.16.tar.bz2</action>
+          <action type="shell_command">sed -i.bak 's/-lcurses/-lncurses/' Makefile</action>
+          <action type="shell_command">make</action>
+          <action type="move_file">
+            <source>samtools</source>
+            <destination>$INSTALL_DIR/bin</destination>
+          </action>
+          <action type="move_file">
+            <source>libbam.a</source>
+            <destination>$INSTALL_DIR/lib</destination>
+          </action>
+        </actions>
+        <action type="set_environment">
+          <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+          <environment_variable name="BAM_LIB_PATH" action="set_to">$INSTALL_DIR/lib</environment_variable>
+        </action>
+      </actions_group>
+    </install>
         <readme>
-Downloads the precompiled 32bit Linux, 64bit Linux, or Mac OS X BLAST+
-binaries from the NCBI, which is faster than performing a local compliation,
-avoids any issues with build dependencies, and is more reproducible between
-installations as there is no variability from the compiler or library versions.
-
-For more details, see:
-http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&amp;PAGE_TYPE=BlastDocs&amp;DOC_TYPE=Download
+          This is the last version of SAMTools to include the 'pileup' command.
+          
+          Program: samtools (Tools for alignments in the SAM format)
+          Version: 0.1.16 (r963:234)
+          
+          Usage:   samtools &lt;command&gt; [options]
+          
+          Command: view        SAM&lt;-&gt;BAM conversion
+         sort        sort alignment file
+         pileup      generate pileup output
+         mpileup     multi-way pileup
+         depth       compute the depth
+         faidx       index/extract FASTA
+         tview       text alignment viewer
+         index       index alignment
+         idxstats    BAM index stats (r595 or later)
+         fixmate     fix mate information
+         glfview     print GLFv3 file
+         flagstat    simple stats
+         calmd       recalculate MD/NM tags and '=' bases
+         merge       merge sorted alignments
+         rmdup       remove PCR duplicates
+         reheader    replace BAM header
+         cat         concatenate BAMs
+         targetcut   cut fosmid regions (for fosmid pool only)
+         phase       phase heterozygotes
         </readme>
-    </package>
+  </package>
 </tool_dependency>