Re: [galaxy-dev] $GALAXY_SLOTS is set incorrectly when using LSF
Awesome! Thanks for the patch - it has been committed as the following changeset. https://bitbucket.org/galaxy/galaxy-central/commits/fcd83883072c64b96ea0f12582fde3d05060b0f4 If anyone else is using something other then LSF, Torque, SLURM, Condor, or SGE - please be aware of this potential problem and send a patch for your platform :). Thanks again, -John On Thu, May 15, 2014 at 3:40 PM, Sytchev, Ilya wrote: > Hi, > > I've noticed that $GALAXY_SLOTS that was always set to 1 when using LSF. > It turns out that LSF specifies the number of parallel slots using > $LSB_DJOB_NUMPROC env variable which isn't checked in > lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh. A > diff that describes the fix is attached. > > Ilya > > > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] $GALAXY_SLOTS is set incorrectly when using LSF
Hi, I've noticed that $GALAXY_SLOTS that was always set to 1 when using LSF. It turns out that LSF specifies the number of parallel slots using $LSB_DJOB_NUMPROC env variable which isn't checked in lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh. A diff that describes the fix is attached. Ilya diff -r 61a3094bd3ed lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh --- a/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Wed May 14 12:15:54 2014 -0400 +++ b/lib/galaxy/jobs/runners/util/job_script/CLUSTER_SLOTS_STATEMENT.sh Thu May 15 16:12:04 2014 -0400 @@ -8,6 +8,8 @@ GALAXY_SLOTS="$NSLOTS" elif [ -f "$PBS_NODEFILE" ]; then GALAXY_SLOTS=`wc -l < $PBS_NODEFILE` +elif [ -n "$LSB_DJOB_NUMPROC" ]; then +GALAXY_SLOTS="$LSB_DJOB_NUMPROC" else GALAXY_SLOTS="1" unset GALAXY_SLOTS_CONFIGURED ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] User information when creating a new user
Hi Neil, The address fields can be populated from User -> Preferences -> Manage your information -> User Addresses. You can also create custom forms - see the "Manage form definitions" link in the admin section. I believe it used to be possible to make custom "User Information" forms required at registration, but unfortunately this isn't working for me in testing, so it may have broken somewhere along the way (this feature is very rarely used). --nate On Wed, May 14, 2014 at 1:45 AM, wrote: > Hi, > when a new user creates a new account they only need an email address > and password. This can be quite tricky to identify the user/demographics > etc at a alter point. Is there a form that a user may complete where he > could add optional data such as name, institution, address etc ? There is a > table (user_address) that stores this information just not sure how/if it's > populated > > Thanks > Neil > > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ > ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Upload a file
I believe Peter is correct - I think this is not documented because in part this is not encouraged. The core team tries very hard to maintain backward compatibility for tool wrappers - I don't think tools that do uploads like this however will receive the same consideration (though that is just my own opinion - I don't speak for the team at large). Certainly you can implement custom upload tools - I have seen other people do it and Jorrit and I did it for the work that eventually landed up in galaxy-extras (e.g. https://bitbucket.org/jmchilton/galaxy-extras/src/be4dd61311a9c08c4e1cb6e85409c155a5abe1cb/tools/data_source/multi_upload.xml?at=extras). If you want to do it - I would just start by copying over upload.xml and upload.py in tools/data_source and start modifying them to do what you want. The code backing up the underlying tag can be found scattered around the code base but some of the key files can be summarized as: upload.py and upload.xml in the data_source file define the user interface and the command-line tool that actually performs the upload. Various infrastructure that aids this includes: A custom tool action (that I believe calls upload.py in data_source) https://bitbucket.org/galaxy/galaxy-central/src/d2300bcd600861bd4b2e5b5ec2d0e0303f7da1f0/lib/galaxy/tools/actions/upload.py?at=default A custom widget in the form builder code: https://bitbucket.org/galaxy/galaxy-central/src/d2300bcd600861bd4b2e5b5ec2d0e0303f7da1f0/lib/galaxy/web/form_builder.py?at=default#cl-140 A special abstract tool parameter: https://bitbucket.org/galaxy/galaxy-central/src/d2300bcd600861bd4b2e5b5ec2d0e0303f7da1f0/lib/galaxy/tools/parameters/grouping.py?at=default#cl-120 Here is one of the key commits of galaxy-extras that enabled multiple upload widgets - hopefully it gives some indication of how the pieces can fit together. https://bitbucket.org/jmchilton/galaxy-extras/commits/e7f99b748e07fb2738cf5e91189111431e2e17dc Hope this helps. -John On Thu, May 15, 2014 at 11:04 AM, Peter Cock wrote: > Hi Robert, > > I'm not sure that is a good idea - the existing upload tool gets > special treatment in many places in Galaxy (e.g. turning a history > into a workflow), and is itself being partly replaced with the newer > Galaxy work (there's a little icon above the tool panel to import > data). > > Peter > > P.S. Don't forget to CC the galaxy-dev list. > > On Thu, May 15, 2014 at 4:59 PM, wrote: >> Hi Peter, >> >> thanks for your reply. I think there is a little misunderstanding: I want to >> implement the upload tool itself. >> I have code from someone else who has used the upload_dataset tag (I cannot >> just use his code because I want to modify something - but when I try to >> re-implement everything myself I need documentation). And my problem is that >> I do not find any documentation for this tag. >> >> Regards, >> Robert >> >> Gesendet: Freitag, 09. Mai 2014 um 16:21 Uhr >> Von: "Peter Cock" >> An: de...@gmx.de >> Cc: "galaxy-dev@lists.bx.psu.edu" >> Betreff: Re: [galaxy-dev] Upload a file >> On Fri, May 9, 2014 at 12:46 PM, wrote: >>> Hi, >>> >>> I am a student who's trying to implement a simple galaxy tool. I am trying >>> to provide the user with the option of uploading a file. I have copied >>> code >>> from another tool ... >> >> The upload tool is special (and separate). Normally the user must >> separately upload their file(s) or import them from a shared library >> BEFORE trying to use any of the analysis tools. >> >> 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Upload a file
Hi Robert, I'm not sure that is a good idea - the existing upload tool gets special treatment in many places in Galaxy (e.g. turning a history into a workflow), and is itself being partly replaced with the newer Galaxy work (there's a little icon above the tool panel to import data). Peter P.S. Don't forget to CC the galaxy-dev list. On Thu, May 15, 2014 at 4:59 PM, wrote: > Hi Peter, > > thanks for your reply. I think there is a little misunderstanding: I want to > implement the upload tool itself. > I have code from someone else who has used the upload_dataset tag (I cannot > just use his code because I want to modify something - but when I try to > re-implement everything myself I need documentation). And my problem is that > I do not find any documentation for this tag. > > Regards, > Robert > > Gesendet: Freitag, 09. Mai 2014 um 16:21 Uhr > Von: "Peter Cock" > An: de...@gmx.de > Cc: "galaxy-dev@lists.bx.psu.edu" > Betreff: Re: [galaxy-dev] Upload a file > On Fri, May 9, 2014 at 12:46 PM, wrote: >> Hi, >> >> I am a student who's trying to implement a simple galaxy tool. I am trying >> to provide the user with the option of uploading a file. I have copied >> code >> from another tool ... > > The upload tool is special (and separate). Normally the user must > separately upload their file(s) or import them from a shared library > BEFORE trying to use any of the analysis tools. > > 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Conditional parameters don't work with radio display
On Thu, May 15, 2014 at 3:48 PM, Hans-Rudolf Hotz wrote: > Hi Peter > > yes, we have been running into the same problem and it is an old problem > which has been reported long time ago by other people as well, Thanks - that's good news (reproducible problem) and bad news then (long standing open problem). I remembered a related issue with boolean parameters (check boxes) not working, which was fixed - but I couldn't find the radio selection problem in my GMail. > eg: > Pieter Neerincx' email from May 2010 (Conditional params don't update > properly when using radio buttons instead of popup menus.): > > I found the email in this thread: > http://dev.list.galaxyproject.org/Galaxy-with-non-SGE-non-Torque-distributed-jobs-tt4136865.html#a4136880 > > > I guess this was reported before Trello was in use and the issue was lost? > > > Hans-Rudolf Thank you for finding that - it looks like it may have been was shortly before I subscribed to the galaxy-dev list. Regards, 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Conditional parameters don't work with radio display
Hi Peter yes, we have been running into the same problem and it is an old problem which has been reported long time ago by other people as well, eg: Pieter Neerincx' email from May 2010 (Conditional params don't update properly when using radio buttons instead of popup menus.): I found the email in this thread: http://dev.list.galaxyproject.org/Galaxy-with-non-SGE-non-Torque-distributed-jobs-tt4136865.html#a4136880 I guess this was reported before Trello was in use and the issue was lost? Hans-Rudolf On 05/15/2014 03:37 PM, Peter Cock wrote: Hello all, I ran into a problem with a conditional select parameter not working when shown as a radio box - despite the HTML having refresh_on_change set: Molecule type of FASTA inputs: protein nucleotide The simple workaround of using a drop-box select box instead worked, e.g. https://github.com/peterjc/galaxy_blast/commit/f70245e25ce171e1508585baea19688cab4786e5 Is this something anyone else has noticed? Should I file an issue? Thanks, Peter -- This is what I was testing with initially, $ hg branch default $ hg log -b default | head changeset: 13855:215f23b27be9 tag: tip user:Carl Eberhard date:Tue Mar 18 16:14:52 2014 -0400 summary: Page-embedded histories: allow embedding the same history more than once by removing the reliance on DOM ids and selecting/traversing based on sibling relation of the history's script I updated, same problem: $ hg log -b default | head changeset: 14501:75be6c49a65d tag: tip user:guerler date:Wed May 14 22:49:44 2014 -0400 summary: Charts: Fix style ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Conditional parameters don't work with radio display
Trello card created - https://trello.com/c/aRbdQB3y. Thanks for the re-bug report guys, sorry if something got lost at some point. -John On Thu, May 15, 2014 at 9:48 AM, Hans-Rudolf Hotz wrote: > Hi Peter > > yes, we have been running into the same problem and it is an old problem > which has been reported long time ago by other people as well, eg: > Pieter Neerincx' email from May 2010 (Conditional params don't update > properly when using radio buttons instead of popup menus.): > > I found the email in this thread: > http://dev.list.galaxyproject.org/Galaxy-with-non-SGE-non-Torque-distributed-jobs-tt4136865.html#a4136880 > > > I guess this was reported before Trello was in use and the issue was lost? > > > Hans-Rudolf > > > > > On 05/15/2014 03:37 PM, Peter Cock wrote: >> >> Hello all, >> >> I ran into a problem with a conditional select parameter not working when >> shown as a radio box - despite the HTML having refresh_on_change set: >> >> >> Molecule type of FASTA inputs: >> > name="seq|dbtype" refresh_on_change="true" value="prot" >> id="seq|dbtype|prot" checked='checked'>> for="seq|dbtype|prot">protein >> > value="nucl" id="seq|dbtype|nucl">> for="seq|dbtype|nucl">nucleotide >> >> >> >> The simple workaround of using a drop-box select box instead worked, e.g. >> >> https://github.com/peterjc/galaxy_blast/commit/f70245e25ce171e1508585baea19688cab4786e5 >> >> Is this something anyone else has noticed? Should I file an issue? >> >> Thanks, >> >> Peter >> >> -- >> >> This is what I was testing with initially, >> >> $ hg branch >> default >> >> $ hg log -b default | head >> changeset: 13855:215f23b27be9 >> tag: tip >> user:Carl Eberhard >> date:Tue Mar 18 16:14:52 2014 -0400 >> summary: Page-embedded histories: allow embedding the same history >> more than once by removing the reliance on DOM ids and >> selecting/traversing based on sibling relation of the history's script >> >> I updated, same problem: >> >> $ hg log -b default | head >> changeset: 14501:75be6c49a65d >> tag: tip >> user:guerler >> date:Wed May 14 22:49:44 2014 -0400 >> summary: Charts: Fix style >> ___ >> 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/ >> >> To search Galaxy mailing lists use the unified search at: >>http://galaxyproject.org/search/mailinglists/ >> > ___ > 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/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Conditional parameters don't work with radio display
Hello all, I ran into a problem with a conditional select parameter not working when shown as a radio box - despite the HTML having refresh_on_change set: Molecule type of FASTA inputs: protein nucleotide The simple workaround of using a drop-box select box instead worked, e.g. https://github.com/peterjc/galaxy_blast/commit/f70245e25ce171e1508585baea19688cab4786e5 Is this something anyone else has noticed? Should I file an issue? Thanks, Peter -- This is what I was testing with initially, $ hg branch default $ hg log -b default | head changeset: 13855:215f23b27be9 tag: tip user:Carl Eberhard date:Tue Mar 18 16:14:52 2014 -0400 summary: Page-embedded histories: allow embedding the same history more than once by removing the reliance on DOM ids and selecting/traversing based on sibling relation of the history's script I updated, same problem: $ hg log -b default | head changeset: 14501:75be6c49a65d tag: tip user:guerler date:Wed May 14 22:49:44 2014 -0400 summary: Charts: Fix style ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] reports page download
Hi Neil I am not aware of any (hidden) download options. I usually go with 'copy-paste' and process in R or manually. Also, if I need specific information which is often not displayed on the reports page I get it directly out of the MySQL/PostgreSQL database. For such cases it is handy to have a read-only user (just to make sure you don't do something bad by accident) Hans-Rudolf On 05/15/2014 08:07 AM, neil.burd...@csiro.au wrote: Hi, is there a way to download the information found on the reports page so it can be used in excel for example? Thanks Neil ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Manual Tool and dependency installation
Hi Ravi To start, have a look at those wiki pages: https://wiki.galaxyproject.org/Admin/Config/ToolDependencies https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies Regards, Hans-Rudolf On 05/14/2014 06:43 PM, Ravi Alla wrote: Hi All, Due to the nature of our cluster we are not allowed to have compilers on our webserver, which is where our galaxy instance runs. Because of this tool dependencies and tools that need to be compiled fail to install through the galaxy tool shed webpage. Is there a way for me to install dependencies and tools manually? For example I am trying to install the GATK2 wrapper. This depends on samtools-0.1.19 from iuc which in turn requires ncurses-5.9. Is there instructions somewhere as to where to install these tools such that they are tied to the GATK2 wrapper? Pardon me if this is a naive question, but I am really out of sorts here. Thank you Ravi ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
