Franco,

You're right, I see a both clean and all rules in the makefile. It looks almost like it's not finding the expected makefile, I'll have to look into that in the morning. As for the download_by_url action, it downloads and extracts the specified file, then changes to the extracted directory.

Could you remind me which changeset revision you're trying to install this repository in?

 --Dave B.

On 2012-12-11 23:10, Franco Caramia wrote:
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" <d...@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 doesn┬╣t..

Any advice on this or at least a link to the pertinent documentation??

Thanks a lot in advance...

Franco


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and notify us immediately by telephone or email.  Peter
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transmission is free of virus or that it has not been
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in its receipt.


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