Franco,
I see the issue, the target_file flag was introduced in
8268:87828175dfe7. If you update to the latest Galaxy dist release, that
tool dependency xml should work just fine.
--Dave B.
On 2012-12-12 01:53, Franco Caramia wrote:
Dave,
It's :
hg log | head
changeset: 8153:5dcbbdfe1087
tag: tip
user: Daniel Blankenberg <d...@bx.psu.edu>
date: Tue Nov 06 12:57:23 2012 -0500
summary: Allow rerun to access hidden datasets.
Thanks,
Franco
On 12/12/12 3:13 PM, "Dave Bouvier" <d...@bx.psu.edu> wrote:
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 doesn¹t..
Any advice on this or at least a link to the pertinent documentation??
Thanks a lot in advance...
Franco
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confidential and/or legally privileged information and is
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are not the intended addressee, any use, distribution,
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and notify us immediately by telephone or email. Peter
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