[galaxy-dev] Choosing between pre-existing file or user-defined file as tool input
Hello, I am building a new tool for Galaxy and I would like for it to have an option for the user to choose his file for input or to use a pre-installed file on the server (in a specific path not defined by the user). Can anyone tell me which is the right parameter type to use in the configuration file? Thank you in advance, Makis Ladoukakis ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Choosing between pre-existing file or user-defined file as tool input
Dear Peter, Thank you for your help. I have used the blastp.loc file and renamed it and altered it in order to keep the same format as in the previous tool. Also I used the same ordering from blastp tool (i.e. 0=value 1=name 2=path). Nevertheless when I run my tool I get the error: Error: Failed to open txt file test_17_Sep_2012 for reading. I have used chmod 777 for my file but the issue still persists. Can you help me please? What could be the problem. Thank you in advance, Makis Ladoukakis Date: Mon, 17 Sep 2012 13:30:34 +0100 Subject: Re: [galaxy-dev] Choosing between pre-existing file or user-defined file as tool input From: p.j.a.c...@googlemail.com To: makis4e...@hotmail.com CC: galaxy-dev@lists.bx.psu.edu On Mon, Sep 17, 2012 at 1:21 PM, Makis Ladoukakis makis4e...@hotmail.com wrote: Hello, I am building a new tool for Galaxy and I would like for it to have an option for the user to choose his file for input or to use a pre-installed file on the server (in a specific path not defined by the user). Can anyone tell me which is the right parameter type to use in the configuration file? Thank you in advance, Makis Ladoukakis The *.loc file mechanism might be a good choice. The BLAST+ wrapper do this to offer you a choice of your own database file from the history, or a system provided database like NR. The associated *.loc file is a simple tabular file of available BLAST databases, and must be filled in by the local Galaxy administrator. Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Tools won't go away even after deleting it from tool_conf.xml
Dear Hans, Thank you for your help. Unfortunately after deleting the file and restarting one of them still remains. Is there anything more I could do? Regards, Efthymios Ladoukakis Date: Thu, 6 Sep 2012 14:25:11 +0200 From: h...@fmi.ch To: makis4e...@hotmail.com CC: galaxy-u...@lists.bx.psu.edu; galaxy-...@bx.psu.edu Subject: Re: Tools won't go away even after deleting it from tool_conf.xml moving to galaxy-dev this is probably related to this issue: http://dev.list.galaxyproject.org/problems-with-labels-in-the-tool-box-and-order-of-the-tools-td4655985.html Hence, try deleting integrated_tool_panel.xml first before you do a restart. Regards, Hans On 09/06/2012 01:29 PM, Makis Ladoukakis wrote: Dear Galaxy users, Has anyone experienced this problem before? In my local instance of Galaxy on a server I've deleted the path of almost all sections with their corresponding tools from tool_conf.xml (wanting to leave my own customized section) but after a restart and a new run of the run.sh there are still two of them (SNP/WGA: Data; Filters andPhenotype Association) left in the tool list with their first tool also appearing. Is there a special setting for those two? Can anyone help me? Thank you, Efthymios Ladoukakis ___ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using reply all in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Update Galaxy instance with Mercurial error
Dear Galaxy users, I am running a Galaxy instance in my institution's server and I want to keep it up to date with the latest release. Nevertheless when i try hg incoming i get the following error: abort: There is no Mercurial repository here (.hg not found)! Most probably the administrator of the server has downloaded the Galaxy-dist directory without the use of Mercurial (I was suspicious of that all along as the directory of the Galaxy installation is named galaxy_dist and not galaxy-dist). Is there another way to update my instance? Thank you, Makis Ladoukakis ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Using quota won't decrease
Dear Galaxy users, I run a local instance of Galaxy on my university's server and I stumbled upon an issue concerning using quota on the upper right corner of the interface. It says I'm using a certain amount of GBs even though I have deleted all raw data from the /galaxy-dist/database/files directory. Has anyone encountered this sort of problem before? Thank you in advance, Makis Ladoukakis ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Galaxy loading never ends
Dear Galaxy users, I have installed a local Galaxy instance in my university's server. Recently I encountered a problem whenever I try to load Galaxy into my browser. When I press the link it starts loading but it never ends resulting with a timeout error. Has anyone encountered this problem before? Thank you in advance, Makis Ladoukakis ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Problem uploading files from filesystem paths
Seems like an error concerning permissions in your galaxy folders. Try: sudo chmod 777 galaxy-dist/ and then try to upload data again. To: galaxy-...@bx.psu.edu From: liisa.ko...@dnalandmarks.ca Date: Tue, 20 Dec 2011 16:22:02 -0500 Subject: [galaxy-dev] Problem uploading files from filesystem paths Hi, I'm trying to upload data to Data Libraries from filesystems paths as Admin. I get the following error. Any ideas? Thanks in advance, Liisa Traceback (most recent call last): File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 394, in __main__() File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 386, in __main__ add_file( dataset, registry, js Job Standard Error Traceback (most recent call last): File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 394, in __main__() File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 386, in __main__ add_file( dataset, registry, json_file, output_path ) File /data/Galaxy/galaxy-dist/tools/data_source/upload.py, line 300, in add_file if datatype.dataset_content_needs_grooming( dataset.path ): File /data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 79, in dataset_content_needs_grooming version = self._get_samtools_version() File /data/Galaxy/galaxy-dist/lib/galaxy/datatypes/binary.py, line 63, in _get_samtools_version output = subprocess.Popen( [ 'samtools' ], stderr=subprocess.PIPE, stdout=subprocess.PIPE ).communicate()[1] File /usr/lib64/python2.6/subprocess.py, line 633, in __init__ errread, errwrite) File /usr/lib64/python2.6/subprocess.py, line 1139, in _execute_child raise child_exception OSError: [Errno 13] Permission denied ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Data upload from a server
Dear Galaxy developers, I have installed a Galaxy local instance on our university's server and I am going to use it to analyze data also uploaded on the same server. Nevertheless the access to the server (and the data) is limited only to those involved with the project so making public urls for them is not an option. Downloading the data to my pc is also not an option as its volume is much greater than my hard drive. Is there another way for Galaxy to access those data? Thank you, Efthymios Ladoukakis ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] Data upload from a server
Dear Galaxy developers, I have installed a Galaxy local instance on our university's server and I am going to use it to analyze data also uploaded on the same server. Nevertheless the access to the server (and the data) is limited only to those involved with the project so making public urls for them is not an option. Downloading the data to my pc is also not an option as its volume is much greater than my hard drive. Is there another way for Galaxy to access those data? Thank you, Efthymios Ladoukakis ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] New tool not recognised unless i reboot
I couldn't find a way to stop the instance through the terminal. Ctrl+C doesn't work so i just close the terminal itself. Is there a command that stops the instance? Date: Wed, 14 Dec 2011 17:32:41 + Subject: Re: [galaxy-dev] New tool not recognised unless i reboot From: p.j.a.c...@googlemail.com To: makis4e...@hotmail.com CC: galaxy-dev@lists.bx.psu.edu 2011/12/14 Makis Ladoukakis makis4e...@hotmail.com: Dear galaxy users, I have downloaded a local instance of Galaxy on my linux distribution (ubuntu) and i am adding new tools i made myself. To add a new tool i follow all the steps (tool definition file and the modification of tool_conf.xml) and run 'sh run.sh' for Galaxy to include it in its interface. Nevertheless when i try to do the same later after i close Galaxy, when i run 'sh run.sh' again i get this error: socket.error: [Errno 98] Address already in use Did you stop the old Galaxy instance which is still running and using that network address? Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
