Hi All,
I have a galaxy installation on an OSX system that has been running fine
with our custom tools. However, now we want to start using for some simple
BAC mapping.
When I go to the main toolshed to install bwa, it lists the following
dependencies.
Repository *package_bwa_0_7_10_039ea20639* revision *5b9aca1e1c07* owned by
*devteam*Repository *package_samtools_1_1* revision *43f2fbec5d52* owned by
*iuc*
However, when running through this process, it fails at the
package_samtools_1_1 stage with an Error. Looking at the INSTALLATION.LOG i
see the following.
#############################################
sed -i 's/-lcurses/-lncurses/' Makefile
STDOUT
#############################################
#############################################
sed -i 's/-lcurses/-lncurses/' Makefile
STDERR
sed: 1: "Makefile": invalid command code M
#############################################
However, looking at the tool_dependencies.xml for this particular package,
I see the following. I've highlighted in yellow a key configuration.
<?xml version="1.0"?>
<tool_dependency>
<package name="samtools" version="1.1">
<install version="1.0">
<actions_group>
<actions architecture="x86_64" os="linux">
<action type="download_by_url">
http://depot.galaxyproject.org/package/linux/x86_64/samtools/samtools-1.1-Linux-x86_64.tgz
</action>
<action type="move_directory_files">
<source_directory>.</source_directory>
<destination_directory>$INSTALL_DIR</destination_directory>
</action>
</actions>
<actions>
<package name="ncurses" version="5.9">
<repository changeset_revision="5e1760c773ba"
name="package_ncurses_5_9" owner="iuc" prior_installation_required="True"
toolshed="https://toolshed.g2.bx.psu.edu"; />
</package>
<package name="zlib" version="1.2.8">
<repository changeset_revision="63a4a902cda2"
name="package_zlib_1_2_8" owner="iuc" prior_installation_required="True"
toolshed="https://toolshed.g2.bx.psu.edu"; />
</package>
<action type="download_by_url">
http://downloads.sourceforge.net/project/samtools/samtools/1.1/samtools-1.1.tar.bz2
</action>
<action type="set_environment_for_install">
<repository changeset_revision="5e1760c773ba"
name="package_ncurses_5_9" owner="iuc" toolshed="
https://toolshed.g2.bx.psu.edu";>
<package name="ncurses" version="5.9" />
</repository>
<repository changeset_revision="63a4a902cda2"
name="package_zlib_1_2_8" owner="iuc" toolshed="
https://toolshed.g2.bx.psu.edu";>
<package name="zlib" version="1.2.8" />
</repository>
</action>
<action type="shell_command">sed -i
's/-lcurses/-lncurses/' Makefile</action>
<action type="shell_command">sed -i -e
"s|CFLAGS=\s*-g\s*-Wall\s*-O2\s*|CFLAGS= -g -Wall -O2
-I$NCURSES_INCLUDE_PATH/ncurses/ -I$NCURSES_INCLUDE_PATH
-L$NCURSES_LIB_PATH|g" Makefile<
/action>
<action type="shell_command">make</action>
<action type="move_file">
<source>samtools</source>
<destination>$INSTALL_DIR/bin</destination>
</action>
</actions>
<action type="set_environment">
<environment_variable action="prepend_to"
name="PATH">$INSTALL_DIR/bin</environment_variable>
<environment_variable action="set_to"
name="SAMTOOLS_ROOT_PATH">$INSTALL_DIR</environment_variable>
</action>
</actions_group>
</install>
So, to me, it sounds like this is trying to compile/install a distribution
meant for linux, but I'm on OSX. I was able to successfully install
samtools 1.2 with no errors.
Is there anyway to update, or modify the code for the BWA installation
recipe to use as a dependency samtools 1.2 rather then 1.1? Or does anyone
have any suggestions on how to get samtools 1.1 to work?
I tried making a bin/ directory and moving a precompiled samtools binary
for 1.1 in the directory. But galaxy didn't seem to recognize that the
dependency was satisfied manually.
Any advice would be greatly appreciated.
Thank you,
-Hans
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