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

Download data by data manager with non generic ftp-proxy
by Tobias Zimmermann 17 Jul '15

17 Jul '15

Dear All, I have some problems with the download of genome files by the data manager. I tried to download some genome files from the UCSC server with the data manager of galaxy ( name: data_manager_fetch_genome_all_fasta, revision: cca219f2b212), but it fails because of a timeout. Our galaxy server is in an internal network without connection to the Internet. To access the Internet we are required to go trough a http-proxy before any web-services can be accessed. The file /shed_tools/toolshed.g2.bx.psu.edu/repos/devteam/data_manager_fetch_genome_all_fasta/cca219f2b212/data_manager_fetch_genome_all_fasta/data_manager/data_manager_fetch_genome_all_fasta.py manages the download of the file. Line 183 shows the problem. Here the FTP item from the python ftplib module tries to establishes the connection to the UCSC ftp server. This connection fails. So here is my question: How can i download data by the data manager with a http-proxy? Regards Tobias

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Data Libraries: Unable to Link to Files When Paths Contain Spaces
by Joseph Brent Greer 17 Jul '15

17 Jul '15

Hi All, We're having problems adding files to data libraries. We'd like to create links to files instead of copying them into Galaxy. We can create links if there aren't spaces in the paths. Also, we can copy files into libraries even if there are spaces in the paths. Unfortunately, we cannot create links to files when their paths contain spaces. The job standard error and miscellaneous information are: Miscellaneous information:uploaded RAW file Traceback (most recent call last): File "/share/galaxy/working/002/2615/set_metadata_hnsR90.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/home/galaxy/Galaxy/galaxy-dist Job Standard Error Traceback (most recent call last): File "/share/galaxy/working/002/2615/set_metadata_hnsR90.py", line 1, in <module> from galaxy_ext.metadata.set_metadata import set_metadata; set_metadata() File "/home/galaxy/Galaxy/galaxy-dist/lib/galaxy_ext/metadata/set_metadata.py", line 80, in set_metadata filename_out = fields.pop( 0 ) IndexError: pop from empty list error We've set allow_library_path_paste = True in galaxy.ini. We've also tried adding "" or '' around the path and get the following error message: Invalid paths: "home/galaxy/Galaxy/galaxy-dist/"/share/projects/2014 Test"" Any help or suggestions would be great. Thanks, Joe Greer Proteomics Center of Excellence Northwestern University

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Ipython behind apache proxy, firefox CORS error
by Jelle Scholtalbers 16 Jul '15

16 Jul '15

Hi Björn, Eric, all, I'm trying to get ipython running on our instance. Without the proxy, e.g. http://myserver:8080 it works fine. However, with the proxy in front (e.g. http://myserver/galaxy) I get this firefox error "11:28:37.793 Cross-Origin Request Blocked: The Same Origin Policy disallows reading the remote resource at http://gbcs-dev:8800/ipython/39958/login?next=%2Fipython%2F39958%2Ftree. (Reason: CORS request failed).1 <unknown>" or on chrome "xhr" request "cancelled". Do you happen to know the correct apache settings to overcome this? I tried a few things, but I ended up with ipython starting, but with a message "cannot connect to websocket". - Jelle

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User is not allowed to view history
by Lina L Faller 16 Jul '15

16 Jul '15

Hi all, I am new to maintaining the galaxy server at my institute and a user emailed me that they get the following error message when trying to view their history: "Either you are not allowed to view this history or the owner of this history has not made it accessible." Is there a way to modify access privileges of the users' histories? Thanks for any advice! ~Lina

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cloudman galaxy - too large volume
by Alexander Vowinkel 16 Jul '15

16 Jul '15

Hi, I get this error on cluster creation: Error creating volume: EC2ResponseError: 400 Bad Request InvalidParameterValueVolume of 2048GiB is too large for volume type standard; maximum is 1024GiB Is there a way to get a volume that big for galaxy? Best, Alexander

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collection problem
by Alexander Vowinkel 15 Jul '15

15 Jul '15

Hi, I have this tool that creates a collection by discovery datasets. It always worked fine, but this time I had 3 Histories, where I ran the tool on three different datasets. When it finished, the collections were empty. The datasets, that should be in the collections however, were there. Is that known? Is that fixed in 15.07? Thanks, Alexander

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cloudlaunch not working
by Alexander Vowinkel 15 Jul '15

15 Jul '15

Hi guys, cloudlounch at launch.usegalaxy.org doesn't work for me anymore. Some hours ago I still was able to start a cluster, but now it seems that the launcher can't connect to my amazon anymore? No machnie get's started. But I'm still able to fetch key pair and placement. Any suggestions what to try? Already: Reloaded page, Restarted PC. Thanks, Alexander

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Nob able to upload even 25MB of file for running metaphlan on public Galaxy sever.
by Prathik KV 15 Jul '15

15 Jul '15

Hi, I am trying to run metaphlan on the Galaxy public website, but even a 25MB file cannot be uploaded for analysis. It says the size is too large. And to run metaphlan on local it is just a nightmare because there is absolutely no tutorial of how to install all the prerequisites for material and metaphlan itself. Please see if you can extend the upload file size to atleast 1GB on the galaxy public server of size or atleast have a tutorial for running metaphlan locally.

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"Variant Annotator" reference genome
by Sarah Maman 15 Jul '15

15 Jul '15

Hello, The Galaxy "Variant Annotator" tool uses this loc file : tool-data/gatk2_picard_indexes.loc This file is available in tool-data/ directory and completed but the dropdown menu of "Variant Annotator" tool is empty. more gatk2_picard_indexes.loc #This is a sample file distributed with Galaxy... oviAri1 oviAri1 Ovis:oviAri1 /bank/Galaxy/oviAri1/current/flat/picard_index/oviAri1.dict ls /bank/Galaxy/oviAri1/current/flat/picard_index/ oviAri1.dict oviAri1.fa oviAri1.fa.fai Could you please tell me where does my mistake ? Kind regards, Sarah Maman -- Sarah Maman INRA - LGC - SIGENAE Chemin de Borde-Rouge - Auzeville - BP 52627 31326 Castanet-Tolosan cedex - FRANCE Tel: +33(0)5.61.28.57.08 Fax: +33(0)5.61.28.57.53

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Galaxy server build
by Benjamin Datko 14 Jul '15

14 Jul '15

Hello All, We am attempting to build a local galxay server and we are looking for some advice. The plan is to purchase a decdicated server to host galaxy and communicate with our IBM System x3755 120 node computer cluster running TORQUE/Maui resource manger and scheduler. Do you have an recomendations on the configuration and adequate hardware for the server. The server will only act as a gateway to users, but will not do any computational heavy lifting. If anyone has had experience with this kind of setup, could you offer any further suggestions? -Ben

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