October 2015 - galaxy-dev - lists.galaxyproject.org

using Bioblend with external authentication
by Hans-Rudolf Hotz 30 Oct '15

30 Oct '15

Hi We would like to start using BioBlend on our production servers (which use external authentication) as well. We have changed the apache conf file by adding <Location "/galaxy/api"> Satisfy Any Allow from all </Location> Nevertheless, we still get the following error, when using one of the example scripts: $ python list_data_libraries.py galaxy-dev.fmi.ch *************** Initiating Galaxy connection Retrieving Data Library list Traceback (most recent call last): File "list_data_libraries.py", line 23, in <module> libraries = gi.libraries.get_libraries() File "/****/lib/python2.6/site-packages/bioblend-0.6.1-py2.6.egg/bioblend/galaxy/libraries/__init__.py", line 216, in get_libraries libraries = Client._get(self, deleted=deleted) File "/****/lib/python2.6/site-packages/bioblend-0.6.1-py2.6.egg/bioblend/galaxy/client.py", line 147, in _get raise ConnectionError(msg) bioblend.galaxy.client.ConnectionError: GET: error 401: '<!DOCTYPE HTML PUBLIC "-//IETF//DTD HTML 2.0//EN">\n<html><head>\n<title>401 Authorization Required</title>\n</head><body>\n<h1>Authorization Required</h1>\n<p>This server could not verify that you\nare authorized to access the document\nrequested. Either you supplied the wrong\ncredentials (e.g., bad password), or your\nbrowser doesn\'t understand how to supply\nthe credentials required.</p>....</body></html>\n', 0 attempts left: None $ Is there anything else we need to change in the conf file, or do we have to do something different? Thank you very much for any help with this Hans-Rudolf -- Hans-Rudolf Hotz, PhD Bioinformatics Support Friedrich Miescher Institute for Biomedical Research Maulbeerstrasse 66 4058 Basel/Switzerland

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Hey I got some problems using galaxy... could you help me?..
by 홍윤지 30 Oct '15

30 Oct '15

Hello, My name is yoong in korean Student I try to use the program namd mapsplice2 on galaxy, but when i write the xml file, i got a problom... the xml file located same place with mapspclie.py And mapsplice has not single output file, so i put the -o option like this python /home/yoong/galaxy/tools/MapSplice-v2.1.9/mapsplice.py -o $alignments.files_path -p 10 --qual-scale phred33 --bam --fusion -c /home/yoong/1_reference/hg19 -x /home/yoong/1_reference/BowtieIndex -1 $input_reads_1 -2 $input_reads_2 the mapsplice2 needs 2 input file, and 2 referens file , then make 8 output files include log folder. if i use that command, result has came out, but it's alwasy failed ... T_T Thank you so much ! Have a nice day !

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new to galaxy
by Olivier CLAUDE 30 Oct '15

30 Oct '15

Hello, My name is olivier, I am a PhD student in biology. I have to run bioinformatical prediction on protein sequences and i chose galaxy to do it. I have some basic skills with linux, and I may have missed some steps. My galaxy server is running for more than one week now; the installation was ok, but I am facing some problems to install some dependencies: - Samtools 0.1.18 returns errors everytime I try to install it: this tool dependencys required tool dependency samtools version 0.1.18 has status error In file included from bgzf.c:32:0: bgzf.h:33:18: fatal error: zlib.h: No such file or directory #include <zlib.h> ^ compilation terminated. make[2]: *** [bgzf.o] Error 1 make[1]: *** [lib-recur] Error 1 make: *** [all-recur] Error 1 - Atlas 3.10.2 2 wont install correctly neither : mkdir: cannot create directory ATLAS/build: No such file or directory - Same goes for Numpy 1.7.1, samtools 1.2, tophat 1.4.0, rsem 1.1.17 Do you have any idea? Or tips? Thank you and have a nice day, M Olivier CLAUDE- PhD Student INSERM/UPMC UMRS ICAN 1166 Equipe 2 Faculté de médecine Pitié-Salpêtrière 91, bld de l'Hôpital - 3ème étage - Porte 305 75013 Paris - FRANCE

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URGENT HELP!
by Ali Al-Shahib 29 Oct '15

29 Oct '15

Hi all I am due to give galaxy training tomorrow and the Galaxy server has gone down. Our galaxy admin is travelling and not responding and I appreciate a quick response to this issue. When I run galaxy_restart.sh I get the following error in web0.pid: migrate.versioning.repository DEBUG 2015-10-28 23:07:47,285 Config: {'db_settings': {'__name__': 'db_settings', 'required_dbs': '[]', 'version_table': 'migrate_version', 'repository_id': 'Galaxy'}} lib/galaxy/model/migrate galaxy.model.migrate.check DEBUG 2015-10-28 23:07:47,296 psycopg2 egg successfully loaded for postgresql dialect Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/buildapp.py", line 35, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/home/galaxy/galaxy-dist/lib/galaxy/app.py", line 52, in __init__ create_or_verify_database( db_url, kwargs.get( 'global_conf', {} ).get( '__file__', None ), self.config.database_engine_options, app=self ) File "/home/galaxy/galaxy-dist/lib/galaxy/model/migrate/check.py", line 104, in create_or_verify_database % ( db_schema.version, migrate_repository.versions.latest, config_arg ) ) Exception: Your database has version '124' but this code expects version '115'. Please backup your database and then migrate the schema by running 'sh manage_db.sh upgrade'. ------ I did then try to do sh manage_db.sh downgrade 115 but I got this error: Traceback (most recent call last): File "./scripts/manage_db.py", line 62, in <module> main( repository=repo, url=db_url ) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/shell.py", line 207, in main ret = command_func(**kwargs) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 202, in downgrade return _migrate(url, repository, version, upgrade=False, err=err, **opts) File "<string>", line 2, in _migrate File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/util/__init__.py", line 159, in with_engine return f(*a, **kw) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/api.py", line 345, in _migrate changeset = schema.changeset(version) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/schema.py", line 80, in changeset changeset = self.repository.changeset(database, start_ver, version) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 225, in changeset changes = [self.version(v).script(database, op) for v in versions] File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/repository.py", line 189, in version return self.versions.version(*p, **k) File "/home/galaxy/galaxy-dist/eggs/sqlalchemy_migrate-0.7.2-py2.6.egg/migrate/versioning/version.py", line 140, in version return self.versions[VerNum(vernum)] KeyError: <VerNum(124)> Any help asap will be greatly appreciated. Ali ************************************************************************** The information contained in the EMail and any attachments is confidential and intended solely and for the attention and use of the named addressee(s). It may not be disclosed to any other person without the express authority of Public Health England, or the intended recipient, or both. If you are not the intended recipient, you must not disclose, copy, distribute or retain this message or any part of it. This footnote also confirms that this EMail has been swept for computer viruses by Symantec.Cloud, but please re-sweep any attachments before opening or saving. http://www.gov.uk/PHE **************************************************************************

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Bismark installation dependencies error
by Jose Juan Almagro Armenteros 28 Oct '15

28 Oct '15

Hello, I have tried to install the last version of Bismark from the toolshed and I got an error while installing. Basically it can't install bowtie and bowtie2 because the folder name is written twice in the download directory. Here is the error: File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 142, in install_and_build_package_via_fabric tool_dependency = self.install_and_build_package( tool_shed_repository, tool_dependency, actions_dict ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/install_manager.py", line 100, in install_and_build_package initial_download=True ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/recipe_manager.py", line 32, in execute_step initial_download=initial_download ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 685, in execute_step dir = self.url_download( work_dir, downloaded_filename, url, extract=True, checksums=checksums ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 223, in url_download extraction_path = archive.extract( install_dir ) File "/steno-internal/projects/galaxy/galaxy-dist/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py", line 89, in extract os.chmod( absolute_filepath, unix_permissions ) [Errno 2] No such file or directory: './database/tmp/tmp-toolshed-mtdM4XBx_/bowtie-0.12.8/bowtie-0.12.8/' As you see "bowtie-0.12.8" is twice in the path and when I check the directory, the last "bowtie-0.12.8" folder doesn't exists. Do you know what could go wrong or an alternative way of specifying the correct path? Best regards, Jose

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Opening Galaxy with a specified History Name -- how to convert the clear text history id to an encrypted id?
by rbrown Brown 28 Oct '15

28 Oct '15

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Re: [galaxy-dev] Hey, I got some problem using galaxy, If you have a time, I hope your help..!!
by Greg Von Kuster 28 Oct '15

28 Oct '15

Hello Yoong, The best place to ask questions like this is the Galaxy Dev mailing list (galaxy-dev(a)lists.galaxyproject.org) There are many developers that support this mailing list, so you will undoutedly receive optimal answers to any of your questions. I’ve forwarded your current questions to the mailing list. Regards, Greg Von Kuster > On Oct 28, 2015, at 12:56 AM, 홍윤지 <yoong0525(a)gmail.com> wrote: > > hey, my name is yoong in korean student . > i'd like to run the program name Mapsplice2, so i made a xml file, and submit that > > this is my xml file.. > > > <tool id="mapsplice" name="Mapsplice" version="2.2.0"> > > <description>MapSplice2 Description</description> > > <command interpreter="python"> > /home/yoong/galaxy/tools/MapSplice-v2.1.9/mapsplice.py -o $alignments.files_path -p 20 --qual-scale phred33 --bam --fusion -c /home/yoong/1_reference/hg19 -x /home/yoong/1_reference/BowtieIndex -1 $input_reads_1 -2 $input_reads_2 > </command> > > <inputs> > <param format="fastq" name="input_reads_1" type="data" label="Source file1"/> > <param format="fastq" name="input_reads_2" type="data" label="Source file2"/> > </inputs> > <outputs> > <data format="bam" name="alignments" label="alignments.bam"/> > <data format="txt" name="deletions" label="deletions.txt"/> > <data format="txt" name="fusions_candidates" label="fusions_candidates.txt"/> > <data format="txt" name="fusions_raw" label="fusions_raw"/> > <data format="txt" name="insertions" label="insertions.txt"/> > <data format="txt" name="junctions" label="junctions.txt"/> > <data format="txt" name="stats" label="stats.txt"/> > </outputs> > <help> > Help > </help> > </tool> > > and, look at the report error, there is no special error... what's was the problom..? Do I something wrong ?... > plz help me...!! Thank you ...

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Error in tool parameters when histories are exported/imported
by Simon Gladman 28 Oct '15

28 Oct '15

Hi all, I've noticed that when I export a history with complex parameter settings for the tool Freebayes, when I re-import it, all of the parameter settings disappear. Does anyone know what is going on? Cheers, Simon. -- Simon Gladman | Bioinformatician Victorian Life Sciences Computation Initiative - LSCC 700 Swanston Street, The University of Melbourne | Victoria 3010 Australia T +61 3 9035 5822 | M 0418 421 077 Mail: simon.gladman(a)unimelb.edu.au Web: http://www.vlsci.org.au

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Re: [galaxy-dev] search paths for custom tools
by Peter Cock 26 Oct '15

26 Oct '15

On Mon, Oct 26, 2015 at 4:37 PM, Tony Schreiner <anthony.schreiner(a)bc.edu> wrote: > I take it the tool_dependencies.xml file goes in the same directory as the > custom tool xml files are. And as such applies to any of them in this > folder? > > Thanks > Tony They need to be in the same tar-ball when the tool is uploaded to the Tool Shed, by convention in the same folder as the tool XML file(s), yes. However, if you are not using the Tool Shed and simply install your tools manually into Galaxy then I'm not 100% sure if you can trigger the env.sh files via the requirement tag in the tool: <requirements> <requirement type="package" version="1.66">biopython</requirement> </requirements> Hopefully one of the Galaxy team can clarify... For local development and deployment outside the Tool Shed, I always installed the dependencies myself at system level, or at the Galaxy Linux user level. Peter

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GCC2016 Training Topic Voting is Open
by Dave Clements 26 Oct '15

26 Oct '15

Hello all, *Voting is now open <http://bit.ly/gcc2016vote>* on what training topics <https://wiki.galaxyproject.org/Events/GCC2016/Training> are offered at GCC2016 Training <https://wiki.galaxyproject.org/Events/GCC2016/Training>. There are nominated topics <https://wiki.galaxyproject.org/Events/GCC2016/Training> spanning from basic usage to advanced deployment. No matter what you do with Galaxy, there are topics for you to choose from. Your vote <http://bit.ly/gcc2016vote> will determine the topics that are offered, which topics should be offered more than once, and which ones should not be scheduled at the same time. Your vote matters. *Topic voting closes November 6.* The Training schedule, including instructors, will be published before early registration opens. *About GCC2016 Training <https://wiki.galaxyproject.org/Events/GCC2016/Training>:* The 2016 Galaxy Community Conference (GCC2016) <https://wiki.galaxyproject.org/Events/GCC2016> will be held June 25-29 at Indiana University <http://indiana.edu/> in Bloomington, Indiana, United States. GCC2016 features two full days of training on June 26-27 <https://wiki.galaxyproject.org/Events/GCC2016/Training>. Each day will have multiple tracks, with each track featuring several sessions throughout the day. Workshops will be hands-on and participants will be strongly encouraged to bring a laptop and follow along. If you work in data-intensive biomedical research, there is no better place than GCC2016 to present your work and to learn from others. As always, please let us know if you have any questions. Thanks, The GCC2016 Exec <https://wiki.galaxyproject.org/Events/GCC2016/Organizers> -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ https://wiki.galaxyproject.org/

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