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Help
by Pasquale Notarangelo 14 Jan '14

14 Jan '14

Hi all, we are two new galaxy users. We have developed 2 new tools and we would connect them into a new workflow. We are able to import both tools and to link them into a workflow but we aren't able to pass the output of the first tool as the input of the second tool. The first tool calls a bash script that produces a simple string (this is the path of the file generated by the script). This is the xnl file of the first tool: <tool id="infnTools_ConcatenateArgumentsTool" name="Concatenate Arguments and generate file Tool"> <description>Concatenate arguments strings and generate file</description> <command interpreter="bash">concatenateArgumentsAndPutFile.sh $inputArguments</command> <inputs> <param name="inputArguments" type="text" label="ARGUMENTS" optional="false"/> </inputs> <outputs> <data format="string" name="output" /> </outputs> </tool> This is the bash script of the first tool (concatenateArgumentsAndPutFile.sh): #!/bin/bash echo "ARGUMENTS:" $@ export PathFile=/tmp/$RANDOM$RANDOM echo $@ > $PathFile echo "PathFile:" $PathFile The xml of the second tool is the following: <tool id="infnTools_InsertBiomasTools" name="InsertJobs and check the status of Biomas"> <description>InsertJobs Biomas Tool and check the status</description> <command interpreter="bash">insertAndCheckBiomasJobs.sh $input </command> <inputs> <param format="string" name="input" type="data" label="Insert path file"/> </inputs> <outputs> <data format="tabular" name="output"/> </outputs> </tool> When we run the workflow the output of the first tool isn't seen as input of the second tool. Into the galaxy history we see this value for the input of the second tool: /home/pasquale/galaxy-dist/database/files/000/dataset_83.dat Also this file is emtpy. How we can resolve the problem? Thanks and best regard Pasquale & Alfonso ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Dott. Pasquale Notarangelo INFN Istituto Nazionale di Fisica Nucleare - Sezione Bari Via Orabona, 4 - 70126 Bari, Italy Tel. ufficio: +39 080-5443194 Interno ufficio: 3194 Mail: pasquale.notarangelo(a)ba.infn.it Skype: pasquale.notarangelo_1985 Msn: pasqualenotarangelo(a)hotmail.it Gmail: notarangelo.pas(a)gmail.com ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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Careful data migration
by Sebastian Schaaf 14 Jan '14

14 Jan '14

Hi @ all, I would like to know if anyone could give me some guidance or hint on how to migrate data 'correctly' if Galaxy already wrote files, worked on the database etc. The situation is that we set up an instance, it was already in use and wrote files e.g. into the directory 'galaxy-dist/database/'. The local space is quite small, but more storage is available via a NFS share. I already wrote a bash script for setting up the connections (and editing the 'universe.wsgi' file accordingly) for the entries 'genome_data_path, 'ftp_upload_dir', 'file_path', 'new_file_path' and 'job_working_directory'. Those should address the most bulky features... The application of that script is fine as long as the Galaxy system has never started before. While applying that on a system that already 'did something', e.g. the files in the 'database/' subdirectory remain there and are not transferred. Anyhow, if Galaxy is started up after the application of the new settings, no error is reported. I wonder how Galaxy now deals with that situation: * Handling data from both sources? (read and/or write?) * Automatic movements of the 'historic' data when touched the next time? * Crashes if those older objects are intended to be read/edited? * Removes them silently from the database? => Is there a procedure/module to used in order to migrate the data? Is it sufficient (and appropriate) just to move all contents of the old folders to the new locations? Did I miss any existing documentation on that issue? The answer(s) may diverge, depending on to which of the five parameters announced above those questions are addressed... Any help appreciated before blowing up our production instance :). Thanks in advance, Best regards, Sebastian -- Sebastian Schaaf, M.Sc. Bioinformatics Faculty Coordinator NGS Infrastructure Chair of Biometry and Bioinformatics Department of Medical Informatics, Biometry and Epidemiology (IBE) University of Munich

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Quota problem
by Thomas Bellembois 14 Jan '14

14 Jan '14

Hello, I am Thomas, IT engineer at the IGFL in France (http://igfl.ens-lyon.fr/) We are running our own Galaxy instance in front of an OGE cluster. Users quota never decrease when they delete items in their history. I have run the scripts in the cleanup_datasets directory but without success. I have no errors in the logs. Any idea ? Regards, Thomas -- Thomas Bellembois, network and system administrator ENS-Lyon/IGFL - 46, Allée d'Italie 69364 LYON CEDEX 07 FRANCE +33 4 26 73 13 67 .The IGFL is a member of the "portail-labos" project (https://portail-labos.ens-lyon.fr/site/) .IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc

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Getting Cufflinks
by Cantarel, Brandi L. 14 Jan '14

14 Jan '14

A colleague has asked me to set up a galaxy server for purpose of running tophat/cufflinks. A recent paper in BMC Genomics would indicate that those tools are integrated into Galaxy. When I download (hg clone) the distribution, I only see tophat, but none of the other tuxedo software. The funny thing that is I google bitbucket, cufflinks, galaxy — I can find a few XML files to run the software but I can’t figure out how to get those files into my local install…I tried the stable and default distribution, but neither included these files… Is there something that I am missing in the download for the ngs-rna tools? Thanks! Brandi Cantarel ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Brandi Cantarel, PhD Bioinformatics Research Scientist Baylor Institute for Immunology Research Baylor Health Care System 214-818-8673 (office) ********************************************************************** This e-mail may contain confidential and/or privileged information. This information is intended only for the use of the individual(s) and entity(ies) to whom it is addressed. If you are the intended recipient, further disclosures are prohibited without proper authorization. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorized copying, disclosure or distribution of the material in this e-mail is strictly forbidden and possibly a violation of federal or state law and regulations. Baylor Health Care System, its subsidiaries, and affiliates hereby claim all applicable privileges related to this information.

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trackster error for viewing rat data (rn5)
by Shu-Yi Su 13 Jan '14

13 Jan '14

Hi, I am trying to view rat data (rn5) using trackster with data format bam or bigwig on our galaxy installation, but it isn't working. It works with other organisms, such as dm3 or hg19. There is error message in the log: 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] "GET /galaxy-dev/api/genomes/rn5?low=0&num=100 HTTP/1.1" 200 - "http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc71049…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1" 10.11.70.120 - - [20/Nov/2013:16:14:21 +0200] "GET /galaxy-dev/api/datasets/83c20bbc7104922b?hda_ldda=hda&data_type=track_config HTTP/1.1" 200 - "http://gbcs-dev/galaxy-dev/visualization/trackster?dataset_id=83c20bbc71049…" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_7_5) AppleWebKit/536.30.1 (KHTML, like Gecko) Version/6.0.5 Safari/536.30.1" galaxy.webapps.galaxy.api.datasets ERROR 2013-11-20 16:14:21,795 Error in dataset API at listing contents: 'BinaryFileReader' object has no attribute 'read_bits64': 'BinaryFileReader' object has no attribute 'read_bits64' Traceback (most recent call last): File "/g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py", line 44, in show is_true( kwd.get( 'retry', False ) ) ) File "/g/funcgen/galaxy-dev/lib/galaxy/webapps/galaxy/api/datasets.py", line 106, in _converted_datasets_state if not data_provider.has_data( chrom ): File "/g/funcgen/galaxy-dev/lib/galaxy/visualization/data_providers/genome.py", line 1078, in has_data all_dat = bbi.query( chrom, 0, 2147483647, 1 ) or \ File "bbi_file.pyx", line 215, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5596) File "bbi_file.pyx", line 222, in bx.bbi.bbi_file.BBIFile.query (lib/bx/bbi/bbi_file.c:5210) File "bbi_file.pyx", line 183, in bx.bbi.bbi_file.BBIFile.summarize (lib/bx/bbi/bbi_file.c:4475) File "bbi_file.pyx", line 248, in bx.bbi.bbi_file.BBIFile._get_chrom_id_and_size (lib/bx/bbi/bbi_file.c:5656) File "bpt_file.pyx", line 76, in bx.bbi.bpt_file.BPTFile.find (lib/bx/bbi/bpt_file.c:1388) File "bpt_file.pyx", line 55, in bx.bbi.bpt_file.BPTFile.r_find (lib/bx/bbi/bpt_file.c:1154) AttributeError: 'BinaryFileReader' object has no attribute 'read_bits64' I also attached the first few lines in our rn5.len: chr1 290094216 chr2 285068071 chr4 248343840 chr3 183740530 chr5 177180328 chr6 156897508 chrX 154597545 chr7 143501887 chr8 132457389 chr9 121549591 chr13 118718031 chr14 115151701 chr15 114627140 chr10 112200500 chr11 93518069 chr17 92503511 chr16 90051983 chr18 87229863 chr19 72914587 chr20 57791882 chr12 54450796 chr4_AABR06109730_random 227955 chrUn_JH620568 73090 chr2_JH620298_random 62026 chr5_JH620330_random 58807 chrUn_JH620520 57992 chrUn_JH620553 56877 chr1_AABR06109393_random 52834 chr18_JH620420_random 51685 chr9_JH620364_random 51490 chrX_JH620445_random 49212 chrUn_JH620623 47760 chr10_JH620371_random 44089 I have looked into this error for a while and still can't figure it out. Any idea or suggestions are very appreciated. Thank you very much. Best regards, Shu-Yi

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BioBlend AND Galaxy: Problem using upload_file_from_server function with an associated role
by Olivia Doppelt 12 Jan '14

12 Jan '14

Hello to all, I'm trying to use the function "/upload_file_from_server/" from the galaxy libraries api of Bioblend. It's working correctly when i don't associate any role to the arguments. However, in our architecture (Institut Pasteur, Paris) it can't be possible that any user may upload any other user's data in their Galaxy Data library. Thus, it is how ""/upload_file_from_server/" is working at the moment. As I understand the problem, it doesn't come from Bioblend itself, as all arguments (as well as roles) are well transmitted on the server side. could somebody help me with that ? Happy new Year !!! and Have a nice day, -- Olivia Doppelt-Azeroual, PhD Tel: 92 15 CIB - Institut Pasteur

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referring to tool_data_tables[] structure
by Dooley, Damion 11 Jan '14

11 Jan '14

I've seen $__app__.tool_data_tables[ 'all_fasta' ].get_fields() )[0][-1] in tool xml templates. Is there a way I can access the tool_data_tables structure from python code too? I see all the initialization stuff happening in https://bitbucket.org/abrenner/galaxy-central/src/f3e736fe03df3a6dd5438c12b… But not seeing where one can access any of these app variables? Regards, Damion

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password problem
by Szendroi Andrea (KING'S COLLEGE HOSPITAL NHS FOUNDATION TRUST) 10 Jan '14

10 Jan '14

To Whom It May Concern: Yesterday, I successfully registered to the Galaxy from my home computer using my: Andrea.Szendroi(a)nhs.net<mailto:Andrea.Szendroi@nhs.net> email. Today, I tried to logon again from my work computer and it did not recognize my password so I tried to reset it and to send my new password to the same email but no email came (I have even checked my junk box). I have tried to reset it several times without any success. Could you please help me? Many thanks, Andrea ******************************************************************************************************************** This message may contain confidential information. If you are not the intended recipient please inform the sender that you have received the message in error before deleting it. Please do not disclose, copy or distribute information in this e-mail or take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Thank you for your co-operation. NHSmail is the secure email and directory service available for all NHS staff in England and Scotland NHSmail is approved for exchanging patient data and other sensitive information with NHSmail and GSi recipients NHSmail provides an email address for your career in the NHS and can be accessed anywhere ********************************************************************************************************************

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I can't use API to create a user!
by xlwang 10 Jan '14

10 Jan '14

When I use API to create a user, I get an error! The command is: #curl -d '{"username":"test","password":"test","email":"123(a)123.com"}' http://myip:8080/api/users?key=my_key I get some information: And I find the api controller source code of users in my galaxy instance, it's different with the source in api document. This is mine: And this is the document: I don't understand how it happens.Please tell me how to fix it.Thank you!

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how to stop extra html file inserted into download zip
by Neil.Burdett＠csiro.au 10 Jan '14

10 Jan '14

Hi, I have a tool that works well. However, when I download the results, the results are zipped up but included into the zip file is the *.html file (with the same name as the tool output) do you know how I can stop this from being zipped up? Thanks Neil

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