Mercurial > repos > saskia-hiltemann > mothur_align_check

changeset 7:dc9aadf1303b draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 8f2b9b6c89892710bd5e0d8e35bcd8b645b0e44f
author saskia-hiltemann
date Tue, 07 Jun 2016 10:41:25 -0400
parents 80b9a27a2563
children 5eb3186cc3b4
files tool_dependencies.xml
diffstat 1 files changed, 2 insertions(+), 70 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Tue Jun 07 07:43:21 2016 -0400
+++ b/tool_dependencies.xml	Tue Jun 07 10:41:25 2016 -0400
@@ -1,75 +1,7 @@
 <?xml version="1.0"?>
 <tool_dependency>
-    <package name="mothur" version="1.36.1">
-        <install version="1.0">
-            <actions>
-                <action type="download_by_url">https://github.com/mothur/mothur/archive/v1.36.1.zip</action>
-                <action type="set_environment_for_install">
-                    <repository changeset_revision="2efc6b3ab0a3" name="package_legacy_blast_2_2_22" owner="saskia2" toolshed="testtoolshed.g2.bx.psu.edu">
-                        <package name="legacy_blast" version="2.2.22" />
-                    </repository>
-                    <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" toolshed="testtoolshed.g2.bx.psu.edu">
-                        <package name="boost" version="1.57" />
-                    </repository>
-                    <repository changeset_revision="03abe628fbe8" name="package_zlib_1_2_8" owner="iuc" toolshed="testtoolshed.g2.bx.psu.edu">
-                        <package name="zlib" version="1.2.8" />
-                    </repository>
-                </action>
-                <action type="shell_command">chmod u+x source/uchime_src/mk</action>
-                <action type="shell_command">
-                    test $(uname) = Linux &amp;&amp;
-                    perl -i.bak -pe 's/(USEREADLINE.+) = yes/$1 = no/; s/TARGET_ARCH \+= -arch x86_64//; s/#(CXXFLAGS.+-mtune=native -march=native -m64)/$1/;' source/makefile ||
-                    true
-                </action>
-                <action type="shell_command">sed -i 's/\ \ \ \ /\t/g' source/makefile;</action>
-                <action type="shell_command">sed -i '141d;151d;152d' source/makefile;</action>
-                <action type="shell_command">sed -i 's/fortranSource//g' source/makefile;</action>
-                <action type="shell_command">sed -i 's/\/usr\/local/${BOOST_ROOT_DIR}\/boost/g' source/makefile;</action>
-                <action type="shell_command">sed -i 's/\${BOOST_LIBRARY_DIR}zlib.a/${ZLIB_ROOT_DIR}\/lib\/libz.a/' source/makefile</action>
-
-                <action type="shell_command">cd source; make -j 2;</action>
-                <action type="move_file">
-                    <source>mothur</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="move_file">
-                    <source>source/uchime</source>
-                    <destination>$INSTALL_DIR/bin</destination>
-                </action>
-                <action type="set_environment">
-                    <environment_variable action="prepend_to" name="PATH">$INSTALL_DIR/bin</environment_variable>
-                </action>
-                <action type="make_directory">$INSTALL_DIR/bin/blast/bin</action>
-                <action type="change_directory">$INSTALL_DIR/bin</action>
-                <action type="shell_command">cd $INSTALL_DIR/bin;mypath=`which blastall`; mypath=`dirname $mypath`; cp $mypath/* ./blast/bin</action>
-            </actions>
-        </install>
-        <readme>
-*Authors &amp; Contacts*
-Jim Johnson
-Peter Briggs
-Iyad Kandalaft | Iyad.Kandalaft@Agr.gc.ca | Agriculture and Agri-Foods Canada
-Kevin Chen | Agriculture and Agri-Foods Canada
-
-*Description*
-
-The Mothur Tool Suite repository provides Galaxy wrappers for the majority of the Mothur tools.  In addition, it downloads and builds the Mothur binaries.
-
-Supports Linux environments such as Redhat/Centos/Ubuntu as well as Mac OSX.
-
-These links provide information for building the Mothur package in most environments.
-
-http://www.mothur.org/wiki/Download_mothur
-
-http://www.mothur.org/wiki/Installation
-http://www.mothur.org/wiki/Makefile_options
-
-*Requirements*
-
-- build tools (make, C libraries, GCC)
-- libncurses-dev(el)
-- simplejson (python library)
-        </readme>
+        <package name="mothur" version="1.36.1">
+            <repository changeset_revision="a2527478856f" name="package_mothur_1_36_1" owner="saskia-hiltemann" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu" />
         </package>
         <package name="legacy_blast" version="2.2.22">
             <repository changeset_revision="2efc6b3ab0a3" name="package_legacy_blast_2_2_22" owner="saskia2" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu" />