Hi Dave,
It does not require it, but it should not fail either as the clean rule is in the makefile.. By removing it I get: make: *** No rule to make target `all'. Stop.
Same problem as before but this time with the 'all' rule... I'm not sure what the <action type="download_by_url" tag does.. Do I need to 'cd' into the unzipped directory?
Thanks,
Franco
On 12/12/12 1:03 PM, "Dave Bouvier" dave@bx.psu.edu wrote:
Franco,
BEDTools, unlike some other packages, does not require the 'make clean' shell command to compile. If you remove that line, the dependency should install without problems.
--Dave B.
On 2012-12-11 21:16, Franco Caramia wrote:
Hi list,
I got the following tool_dependencies.xml file failing:
<?xml version="1.0"?>
<tool_dependency> <package name="bedtools" version="2.17.0"> <install version="1.0"> <actions> <action type="download_by_url" target_filename="bedtools-2.17.0.tar.gz" >http://bedtools.googlecode.com/files/BEDTools.v2.17.0.tar.gz</action> <action type="shell_command">make clean</action> <action type="shell_command">make all</action> <action type="move_directory_files"> <source_directory>bin</source_directory> <destination_directory>$INSTALL_DIR/bin</destination_directory> </action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> GCC version 4.1 or greater is recommended. 3.x versions will typically not compile BEDTools </readme> </package> </tool_dependency>
The error given is:
############################################# make clean STDOUT
#############################################
############################################# make clean STDERR make: *** No rule to make target clean'. Stop. #############################################
I basically just copied the example code from the Galaxy wiki for R:
<?xml version="1.0"?>
<tool_dependency> <set_environment version="1.0"> <environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> </set_environment> <package name="R" version="2.15.1"> <install version="1.0"> <actions> <action type="download_by_url">http://CRAN.R-project.org/src/base/R-2/R-2.15.1.tar.gz </action> <action type="shell_command">./configure --prefix=$INSTALL_DIR</action> <action type="shell_command">make</action> <action type="set_environment"> <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable> </action> </actions> </install> <readme> You need a FORTRAN compiler or perhaps f2c in addition to a C compiler to build R. </readme> </package> </tool_dependency>
I have found no documentation to what the tag <action type="download_by_url"> does... I have asumed it downloads, unzips and moves into the unzipped directory.. But apparently it doesn¹t..
Any advice on this or at least a link to the pertinent documentation??
Thanks a lot in advance...
Franco
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