problems in integrating tools to GALAXY
Hi, Dear all, I am trying to integrate a perl script to GALAXY, and here are the problems. I have a tool configuration xml file called abc.xml located at tools/myTools directory, which calls a perl scripts called toolExample.pl. 1 <tool id="abc" name="abc"> 2 <command interpreter="perl">toolExample.pl $input $output</command> 3 <inputs> 4....... 5...... Inside the toolExample.pl, I am using some linux system command such as "wc" and also "BEDTools/windowBed". The BEDTools executables are configured correctly in my local linux machine, and when I type "which windowBed" it can give me back the path correctly. When I run toolExample.pl outside galaxy in the terminal, everything looks correct; but when I run galaxy, it gave me the nonsense results ( all 0) and it seems that GALAXY has problems in recognizing either the windowBed excutable file or the linux system command "wc" or maybe both. To let GALAXY recognize "windowBed", I tried to put the windowBed executable copied to myTools directory and add the following <requirements>tags to the abc.xml file, but it doesn't seem to be working. ..... <requirements> <requirement type="binary">windowBed</requirement> </requirements> .... Could anyone please help me figure out what was wrong? How can I fix the problem? Thank you very much in advance! Best, Jenny
Hi Jenny Do you actually get an error message? like: "tool not found" First, try to find out what is actually not working in your script by adding some debugging comments (eg: print "wc run correctly"; etc) Next, just to get it working, provide the full path for each tool in the system command lines in your perl script. Once you have figured out the problem, you can remove them again. Another point to consider: Are you running Galaxy as 'yourself' or as user galaxy? The user galaxy might not have all the required binaries in its path. You can add them by modifying the 'run.sh' script (eg: PATH=$PATH:/mytools/BEDTools ). Regards, Hans On 08/14/2012 08:43 PM, Jenny wrote:
Hi, Dear all,
I am trying to integrate a perl script to GALAXY, and here are the problems.
I have a tool configuration xml file called abc.xml located at tools/myTools directory, which calls a perl scripts called toolExample.pl. 1 <tool id="abc" name="abc"> 2 <command interpreter="perl">toolExample.pl $input $output</command> 3 <inputs> 4....... 5......
Inside the toolExample.pl, I am using some linux system command such as "wc" and also "BEDTools/windowBed". The BEDTools executables are configured correctly in my local linux machine, and when I type "which windowBed" it can give me back the path correctly. When I run toolExample.pl outside galaxy in the terminal, everything looks correct; but when I run galaxy, it gave me the nonsense results ( all 0) and it seems that GALAXY has problems in recognizing either the windowBed excutable file or the linux system command "wc" or maybe both.
To let GALAXY recognize "windowBed", I tried to put the windowBed executable copied to myTools directory and add the following <requirements>tags to the abc.xml file, but it doesn't seem to be working. ..... <requirements> <requirement type="binary">windowBed</requirement> </requirements> ....
Could anyone please help me figure out what was wrong? How can I fix the problem? Thank you very much in advance!
Best, Jenny ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
participants (2)
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Hans-Rudolf Hotz -
Jenny