Re: [galaxy-user] Batch jobs...
On Fri, Oct 26, 2012 at 7:46 AM, Björn Grüning wrote: > Hi Neil, > > if you run your workflow, there is small little symbol/icon (looks like > papers). If you click these ... you can select multiple input files at > once. Also you can probably use the Galaxy API for your task [1]. > Well this would only work if one of the 2 input files Neil mentions is fix. Multiple input files selection doesn't work for workflows with more than one input files, unless there is only one input changing in each run and the rest are fix. At least as far as I know. Using the API might be your only option if this is the case. --Carlos ___ 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/
Re: [galaxy-user] Import files from filesystem path : No redundance?
On Oct 26, 2012, at 10:32 AM, julie dubois wrote: > Hi all, > I have used the option "Import files from filesystem path" to import a > complete arborescence of directories and files in one Data Library of Galaxy. > > Lot of files and sub-directories wil add to this arborescence. > I've hoped import those changes in my data library with the option : add > datasets, then indicate the path of this arborescence at the option "import > from filesystem path". > But when I use this way, Galaxy re-import all arborescence : the new files > and sub-directories AND all already imported directories and files! > > Is there a way to import just the new files without know a priori which are > new in my arborescence? > Thanks. Hi Julie, This function is designed for single-time imports. To maintain synchronization between your filesystem and Galaxy, I'd suggest writing an API script. --nate > > Julie > ___ > 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/ ___ 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/
[galaxy-user] Import files from filesystem path : No redundance?
Hi all, I have used the option "Import files from filesystem path" to import a complete arborescence of directories and files in one Data Library of Galaxy. Lot of files and sub-directories wil add to this arborescence. I've hoped import those changes in my data library with the option : add datasets, then indicate the path of this arborescence at the option "import from filesystem path". But when I use this way, Galaxy re-import all arborescence : the new files and sub-directories AND all already imported directories and files! Is there a way to import just the new files without know a priori which are new in my arborescence?* *Thanks. Julie* * ___ 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/
Re: [galaxy-user] Batch jobs...
Hi Neil, if you run your workflow, there is small little symbol/icon (looks like papers). If you click these ... you can select multiple input files at once. Also you can probably use the Galaxy API for your task [1]. Happy research! Bjoern [1] http://wiki.g2.bx.psu.edu/Learn/API > Hi, >I've created a workflow that works well. The workflow accepts 2 input > files. After uploading all my input files (there is a lot). How can I batch > the process, because I don't want to select files manually and run each job > manually. Is there a way to batch this action? > > Thanks > Neil > ___ > 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/ -- Björn Grüning Albert-Ludwigs-Universität Freiburg Institute of Pharmaceutical Sciences Pharmaceutical Bioinformatics Hermann-Herder-Strasse 9 D-79104 Freiburg i. Br. Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ Tel.: +49 761 203-4872 Fax.: +49 761 203-97769 E-Mail: bjoern.gruen...@pharmazie.uni-freiburg.de Web: http://www.pharmaceutical-bioinformatics.org/ ___ 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/
[galaxy-user] Manage Jobs...
Hi I have a local install of Galaxy running on my desktop. When I'm running a task I expected to see the process under "Admin->Manage Jobs" but it doesn't appear here. Do I need to set something to see the processes here? Neil ___ 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/
[galaxy-user] Batch jobs...
Hi, I've created a workflow that works well. The workflow accepts 2 input files. After uploading all my input files (there is a lot). How can I batch the process, because I don't want to select files manually and run each job manually. Is there a way to batch this action? Thanks Neil ___ 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/
