Mercurial > repos > saskia-hiltemann > mothur_align_check

changeset 2:fb85f0b4bdfa draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ecf9d5a72087f0a50a97b183162f10b81dfd9160-dirty
author saskia-hiltemann
date Mon, 06 Jun 2016 10:39:18 -0400
parents 7933347d5b4a
children 52a70ef5248c
files tool_dependencies.xml
diffstat 1 files changed, 13 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- a/tool_dependencies.xml	Mon Jun 06 09:57:31 2016 -0400
+++ b/tool_dependencies.xml	Mon Jun 06 10:39:18 2016 -0400
@@ -3,6 +3,9 @@
     <package name="blast" version="2.2.22">
         <repository changeset_revision="4f8b2f842678" name="package_legacy_blast_2_2_22" owner="saskia-hiltemann" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu" />
     </package>
+    <package name="boost" version="1.57">
+        <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" prior_installation_required="True" toolshed="testtoolshed.g2.bx.psu.edu" />
+    </package>
     <package name="mothur" version="1.36.1">
         <install version="1.0">
             <actions>
@@ -10,16 +13,21 @@
                 <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/;' Mothur.source/makefile ||
+                    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/g' source/makefile;</action>
+
                 <action type="shell_command">cd source; make -j 2;</action>
                 <action type="move_file">
                     <source>source/mothur</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
                 <action type="move_file">
-                    <source>Mothur.source/uchime</source>
+                    <source>source/uchime</source>
                     <destination>$INSTALL_DIR/bin</destination>
                 </action>
                 <action type="set_environment">
@@ -30,6 +38,9 @@
                     <repository changeset_revision="4f8b2f842678" name="package_legacy_blast_2_2_22" owner="saskia-hiltemann" toolshed="testtoolshed.g2.bx.psu.edu">
                         <package name="blast" version="2.2.22" />
                     </repository>
+                    <repository changeset_revision="bd65814f17c5" name="package_boost_1_57" owner="iuc" toolshed="https://testtoolshed.g2.bx.psu.edu">
+                        <package name="boost" version="1.57" />
+                    </repository>
                 </action>
                 <action type="make_directory">$INSTALL_DIR/bin/blast/bin</action>
                 <action type="change_directory">$INSTALL_DIR/bin</action>