February 2013 - galaxy-dev - lists.galaxyproject.org

History not updating automatically
by Sajoscha Sauer 01 Feb '13

01 Feb '13

Hi list, I have a weird problem after updating to the latest version. After doing the update as usual, the history panel is not updating automatically anymore. And when I press refresh, I get an javascript popup saying: Error getting history updates from the server. Forbidden Also, in the log I see the following: galaxy.web.framework WARNING 2013-01-28 12:30:01,673 User logged in as '(null)' externally, but has a cookie as 'sauer(a)embl.de' invalidating session We are using LDAP to connect to Galaxy, but I don't know if this has something to do with the problem. As I said, it was working perfectly fine before the update. Does someone know the problem or has any ideas? Thanks for your help, Sajoscha

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How to use the API when using a proxy server
by Anthonius deBoer 01 Feb '13

01 Feb '13

Hi, I am trying to use the API with my galaxy server running behind a proxy server. How do I pass username/password information to the API so it can actually run? If I use the regular API calls I get a access denied... Thanks Thon

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install Galaxy in Windows (URGENT)
by Prasun Dutta 01 Feb '13

01 Feb '13

Hi, I have Windows Vista and 8 in two separate laptops. I need to install a local version of Galaxy server in both the systems. I am unable to understand or follow the instructions given in your website (http://wiki.galaxyproject.org/Admin/Get%20Galaxy) Could you kindly help me or just explain me stepwise how to install it in my system? Regards, Prasun Dutta MSc (Bioinformatics) School of Biological Sciences University of Edinburgh, UK

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loading file into local galaxy for first time
by Hakeem Almabrazi 01 Feb '13

01 Feb '13

Hi, I just finished installed a local galaxy. I tried to load a simple small fasta file using Load Data and it is still showing as Queued (Blue). It should not take it that much to load. SO I assumed I have some issues in my installation. Can someone tell me what could ne the issue? Or how to go about debugging it? By the way, where the logs in galaxy get stores at? Appreciate your help....

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install reference genome Bwa and Bowtie!
by Hakeem Almabrazi 01 Feb '13

01 Feb '13

Hi, I just installed Galaxy in local Centos Vm. I did my best to get everything working ( I think). I followed the instructions in this Wiki (http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup) to install reference genomes for the tools Bwa and Bowtie. Here is what I did in details: 1. I installed all the software and added them to the PATH and everything seems to be working. 2. Then I created the indices as explained. 3. I put all the indices in the same recommended directory structure and gave all access rights to the Galaxy user which runs the Galaxy server. 4. I created the loc files (bowtie_indices.loc and bowtie_indices_color.loc and bwa_index.loc) and populate them with the recommended contents) and place them in ~/tool_data/ folder. 5. I copied the xml and py files from this location and put them into ~/tools/sr_mapping/.... https://bitbucket.org/galaxy/galaxy-dist/src/da9d740fce31/tools/sr_mapping This step was not mentioned in the instruction but I thought this might be the cause. 6. I restarted the server. Once I select NGS:Mapping tool and Bwa or Bowtie I do not see the reference genome in the list. Can someone tell me what I missed or how to go about debugging it? I appreciate any kind of help....

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February 2013 Galaxy Update
by Dave Clements 01 Feb '13

01 Feb '13

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How do I allow a large group of users to RUN my workflow without them having to make a local copy
by Anthonius deBoer 01 Feb '13

01 Feb '13

Hi, I am trying to build some workflows for people that are part of a group and I want to share that workflow with them, so that they can run the workflow without having to make a local copy for them self. It seems I can only share a workflow in that manner with an individual, and not with a group... Am I reading that correctly? It seems strange not to be able to share workflows with groups if you can share them with individual users.. I also have to know the exact username (email) for each user, rather than being able to choose it from a list... Is there any reason for this or is just underdeveloped? Thanks Thon

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Error loading a BAM file -- dataset needs grooming
by Maureen J. Donlin 01 Feb '13

01 Feb '13

Hi, I tried to load a BAM file into our local instance of Galaxy but get the following error. I had preloaded the genome to which it was aligned and the bai file. Do I have to load these using a different method and the file upload? Thanks, Maureen Traceback error: Traceback (most recent call last): File "/work/apps/galaxy/tools/data_source/upload.py", line 384, in <module> __main__() File "/work/apps/galaxy/tools/data_source/upload.py", line 373, in __main__ add_file( dataset, registry, json_file, output_path ) File "/work/apps/galaxy/tools/data_source/upload.py", line 312, in add_file if link_data_only == 'copy_files' and datatype.dataset_content_needs_grooming( output_path ): File "/work/apps/galaxy/lib/galaxy/datatypes/binary.py", line 113, in dataset_content_needs_grooming version = self._get_samtools_version() File "/work/apps/galaxy/lib/galaxy/datatypes/binary.py", line 97, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File "/usr/lib64/python2.6/subprocess.py", line 639, in __init__ errread, errwrite) File "/usr/lib64/python2.6/subprocess.py", line 1228, in _execute_child raise child_exception OSError: [Errno 2] No such file or directory -- Maureen J. Donlin, Ph.D. Research Associate Professor Dept. of Biochemistry & Molecular Biology Dept. of Molecular Microbiology & Immunology Saint Louis University School of Medicine 507 Doisy Research Center Office: 314-977-8858 Cell: 314-750-2345

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How to call a cgi web page in a galaxy folder from a script?
by Zinonas Antoniou 01 Feb '13

01 Feb '13

Hello, Now I have a web page (cgi) in a server like www.example.com/myexample.py I want to have the myexample.py file under a galaxy folder. Then, how will I call it inside a script in galaxy? Thank you in advance, Zinon

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Patch for RepeatMasker.xml for RepeatMasker 3.3.0
by Guest, Simon 01 Feb '13

01 Feb '13

Dear Galaxians, We are using Galaxy with RepeatMasker 3.3.0. I don't know whether that is the expected version, as I can't find any statement about what is required in the Galaxy tool dependencies for RepeatMasker. Anyway, when a job is submitted with no repeats, RepeatMasker 3.3.0 doesn't create the various output and summary files (.tbl, .out.gff, .out.html, .masked). This causes the Galaxy job to fail with an error message that scares the end user. I attach a patch to handle this case, by touch'ing these files before trying to copy them. Now such jobs succeed with empty output. I think this is clearer, and certainly less scary. Is there a better mechanism for me to contribute such fixes other than posting patches on this list? cheers, Simon ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================

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