Picard installation problem
Hello all, I get troubles installing Picard. In short is there a dedicated link with precise instructions on how to install it on Galaxy? I spent hours trying to install it and if I made a subtle step forward in the installation, I am still stuck with exceptions when trying to run any picard tool. My first problem was to have a link to a built-in reference genome. I finally fixed it. I explain my solution here for interested persons. (1) create the 'dict' file from your reference fasta file by using the following picard tool: java -jar CreateSequenceDictionary.jar -R=<ref-genome.fa> -O=<ref-genome.dict> (2) modify the picard.loc index file to point to the correct location (3) -- the step that took me hours to find -- modify the all-fasta.loc file to point to the correct location. Second -and still unsolved- problem: When i try to run a picard tool, I get the following exception: File "/home/hg/Galaxy/galaxy-dist/tools/picard/picard_wrapper.py", line 40 class PicardBase(): ^ SyntaxError: invalid syntax I downloaded the last release of picard (picard-tools-1.48) and put all the jars file in tool-data/shared/jars/ permission of the files are : -rw-r--r-- 1 apache adm I suspect that galaxy can't find the jars file (i get the same error if I remove them from that location). Am I missing something? Should I precise something about the classpath in galaxY? Thank you for your help, Colin
Colin;
Second -and still unsolved- problem: When i try to run a picard tool, I get the following exception:
File "/home/hg/Galaxy/galaxy-dist/tools/picard/picard_wrapper.py", line 40 class PicardBase(): ^ SyntaxError: invalid syntax
What version of Python are you running? This appears to be a syntax error from an older version: $ python2.7 Python 2.7.1+ (r271:86832, Apr 11 2011, 18:13:53) [GCC 4.5.2] on linux2 Type "help", "copyright", "credits" or "license" for more information.
class Test(): ...
$ python2.4 Python 2.4.3 (#1, Nov 11 2010, 13:30:19) [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
class Test(): File "<stdin>", line 1 class Test(): ^ SyntaxError: invalid syntax
If you're using 2.4 it's well worth upgrading to 2.6 or 2.7. Hope this helps, Brad
If i type python in a terminal, it says that it uses the version 2.6.7. And it succeed in creating a class Test(). is it possible that my galaxy distribution is using an older version? is there a way to check what python version does galaxy use? thanks colin 2011/8/14 Brad Chapman <chapmanb@50mail.com>
Colin;
Second -and still unsolved- problem: When i try to run a picard tool, I get the following exception:
File "/home/hg/Galaxy/galaxy-dist/tools/picard/picard_wrapper.py", line 40 class PicardBase(): ^ SyntaxError: invalid syntax
What version of Python are you running? This appears to be a syntax error from an older version:
$ python2.7 Python 2.7.1+ (r271:86832, Apr 11 2011, 18:13:53) [GCC 4.5.2] on linux2 Type "help", "copyright", "credits" or "license" for more information.
class Test(): ...
$ python2.4 Python 2.4.3 (#1, Nov 11 2010, 13:30:19) [GCC 4.1.2 20080704 (Red Hat 4.1.2-48)] on linux2 Type "help", "copyright", "credits" or "license" for more information.
class Test(): File "<stdin>", line 1 class Test(): ^ SyntaxError: invalid syntax
If you're using 2.4 it's well worth upgrading to 2.6 or 2.7. Hope this helps, Brad
Colin;
If i type python in a terminal, it says that it uses the version 2.6.7. And it succeed in creating a class Test().
is it possible that my galaxy distribution is using an older version? is there a way to check what python version does galaxy use?
Unless you've modified the run.sh script, Galaxy uses whatever 'python' points to on the PATH. The best way to check is manually: login as the user running Galaxy and see what version 'python' gives you. If your instance is running on a cluster, you may also want to check that the proper PATH is passed to the workers. Hope this helps, Brad
Hi, Colin. Sorry you are having such problems. There's a lot of detailed documented that's just not yet written. As you discovered, Picard tools expect the individual Picard jar files to be in tool-data/shared/jars/ eg in one of the tools like rgPicardMarkDupes.xml you'll see -j "${GALAXY_DATA_INDEX_DIR}/shared/jars/MarkDuplicates.jar" And as you figured out .loc files need to be edited to suit your local install. There's http://wiki.g2.bx.psu.edu/Admin/Data%20Integration. There are some changes since that was written, but those .loc files must have valid paths to local copies of the reference genome and index files. (Be careful that you only use tabs to mark columns when you edit them or mysterious breakage will follow) The defaults in tool_data_table.xml should work fine.There are scripted (eg https://bitbucket.org/afgane/mi-deployment ) ways to set these up - it's fiddly by hand but once you've got one genome working, adding new ones is not so bad. On Sun, Aug 14, 2011 at 9:01 PM, colin molter <colin.molter@gmail.com> wrote:
Hello all, I get troubles installing Picard. In short is there a dedicated link with precise instructions on how to install it on Galaxy? I spent hours trying to install it and if I made a subtle step forward in the installation, I am still stuck with exceptions when trying to run any picard tool. My first problem was to have a link to a built-in reference genome. I finally fixed it. I explain my solution here for interested persons. (1) create the 'dict' file from your reference fasta file by using the following picard tool: java -jar CreateSequenceDictionary.jar -R=<ref-genome.fa> -O=<ref-genome.dict> (2) modify the picard.loc index file to point to the correct location (3) -- the step that took me hours to find -- modify the all-fasta.loc file to point to the correct location. Second -and still unsolved- problem: When i try to run a picard tool, I get the following exception:
File "/home/hg/Galaxy/galaxy-dist/tools/picard/picard_wrapper.py", line 40 class PicardBase(): ^ SyntaxError: invalid syntax
I downloaded the last release of picard (picard-tools-1.48) and put all the jars file in tool-data/shared/jars/ permission of the files are : -rw-r--r-- 1 apache adm I suspect that galaxy can't find the jars file (i get the same error if I remove them from that location). Am I missing something? Should I precise something about the classpath in galaxY? Thank you for your help, Colin
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-- Ross Lazarus MBBS MPH; Associate Professor, Harvard Medical School; Director of Bioinformatics, Channing Lab; Tel: +1 617 505 4850; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444;
participants (3)
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Brad Chapman -
colin molter -
Ross