[galaxy-dev] attribute holding history dataset number

2011-01-19 Thread Leandro Hermida
Hello, In your history where you have a piece of data for e.g.: 1: my_file.txt The number 1 what is the attribute for that so that I can use that in a tool configuration? I tried for example $input1.dbkey but that just yields a ? mark best, Leandro

Re: [galaxy-dev] attribute holding history dataset number

2011-01-30 Thread Leandro Hermida
H Nate, Where can I find the wiki page which lists all of the attributes available for tool objects? (e.g. input params, ouput, etc.) best, Leandro On Thu, Jan 27, 2011 at 6:07 PM, Nate Coraor n...@bx.psu.edu wrote: Leandro Hermida wrote: Hello, In your history where you have a piece

Re: [galaxy-dev] [galaxy-user] Peep view for history elements broken on IE?

2011-01-31 Thread Leandro Hermida
Hi everyone, I posted a similar thread back in August http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-August/003224.html There are a couple web UI issues with Galaxy when using IE, like as mentioned in this thread in the history pane data items the link is missing and you cannot expand them

[galaxy-dev] Tools to organize long histories

2011-02-02 Thread Leandro Hermida
Hi everyone, Are there any capabilities or tools in Galaxy to organize long histories with many datasets? best, Leandro ___ galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

Re: [galaxy-dev] MySQL 2 Postgres

2011-03-31 Thread Leandro Hermida
Hi, It's built into mysqldump, just add the following option to your mysqldump command: --compatible=postgresql -Leandro On Wed, Mar 30, 2011 at 3:20 PM, SHAUN WEBB swe...@staffmail.ed.ac.ukwrote: We are experiencing issues with workflows where jobs are running before the previous step is

[galaxy-dev] reason/advantages for making Galaxy proxy using mod_rewrite instead of mod_proxy

2011-04-08 Thread Leandro Hermida
Hi all, Sorry if this question has been asked before searched and couldn't find anyone specifically talking about this. In the Galaxy wiki under https://bitbucket.org/galaxy/galaxy-central/wiki/Config/ApacheProxy there are instructions for setting up Galaxy behind a web server proxy. I wondered

Re: [galaxy-dev] reason/advantages for making Galaxy proxy using mod_rewrite instead of mod_proxy

2011-04-08 Thread Leandro Hermida
, I have seen before configurations with mod_proxy and mod_rewrite directives together doing the same thing I was wondering why! :) best, Leandro On Fri, Apr 8, 2011 at 12:22 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi all, Sorry if this question has been asked before searched

Re: [galaxy-dev] reason/advantages for making Galaxy proxy using mod_rewrite instead of mod_proxy

2011-04-08 Thread Leandro Hermida
/packed/$1 [L] best, Leandro On Fri, Apr 8, 2011 at 1:55 PM, Leandro Hermida soft...@leandrohermida.comwrote: Hi again, After a bit more research I guess I can see why -- since as you show in the instructions you also intend to serve static content via the proxy server and this requires using

Re: [galaxy-dev] MySQL to PostgreSQL migration scripts available here

2011-04-13 Thread Leandro Hermida
Hi Louise, Sorry if this is a bad recommendation and if you already tried it and it doesn't work for Galaxy, but did you know that the MySQL database dump program mysqldump has a feature to dump the entire database properly for import into PostgreSQL? mysqldump --compatible=postgresql [galaxy db

[galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

2011-04-15 Thread Leandro Hermida
Hi everyone, I was wondering what would be the way in Galaxy to program the following: - User clicks on a tool and form is displayed - They use a select multi menu in the form to pick lets say X multiple datasets from their history - When they click submit the tool launches X number of jobs in

Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

2011-04-15 Thread Leandro Hermida
, 2011, at 8:14 AM, Leandro Hermida wrote: Hi everyone, I was wondering what would be the way in Galaxy to program the following: - User clicks on a tool and form is displayed - They use a select multi menu in the form to pick lets say X multiple datasets from their history - When

Re: [galaxy-dev] Getting tool dirpath in a Python code file

2011-04-15 Thread Leandro Hermida
Hi sorry to ping again, but do any of the Galaxy developers have advice/recommended approach for the problem in this thread? On Thu, Apr 14, 2011 at 3:56 PM, Leandro Hermida soft...@leandrohermida.com wrote: On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Thu

Re: [galaxy-dev] Getting tool dirpath in a Python code file

2011-04-15 Thread Leandro Hermida
On Fri, Apr 15, 2011 at 7:27 PM, Peter Cock p.j.a.c...@googlemail.comwrote: On Thu, Apr 14, 2011 at 2:56 PM, Leandro Hermida soft...@leandrohermida.com wrote: On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock p.j.a.c...@googlemail.com wrote: For standard Python tools in Galaxy, I'm using

Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

2011-04-21 Thread Leandro Hermida
green from my perspective. I think functionality like this built into the workflow editor would be a great addition. Dave On Apr 15, 2011, at 8:14 AM, Leandro Hermida wrote: Hi everyone, I was wondering what would be the way in Galaxy to program the following: - User clicks

Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

2011-04-27 Thread Leandro Hermida
... is it possible to execute a tool job via the Galaxy API just like someone does via the UI? Could I then have a tool script that wraps this programmatic execution of X tool jobs via the API? regards, Leandro On Apr 21, 2011, at 7:49 AM, Leandro Hermida wrote: Hi again, Sorry

Re: [galaxy-dev] Does REMOTE_USER have to be an email address?

2011-04-27 Thread Leandro Hermida
to Galaxy, if anyone needs help with such an LDAP configuration please ask me I have it working with Apache mod_authnz_ldap against Active Directory. regards, Leandro On Fri, Apr 8, 2011 at 7:07 PM, Leandro Hermida soft...@leandrohermida.comwrote: Hello, When returning REMOTE_USER env var from

[galaxy-dev] User Name not set with external LDAP authentication

2011-04-27 Thread Leandro Hermida
Hi, Just wondering if I got my setup right, I have Galaxy front-ended by Apache doing the static caching, proxying and LDAP auth. What's nice is that user's don't have to be created by an admin if the user authenticates and authorizes properly against the LDAP config then Galaxy will

Re: [galaxy-dev] User Name not set with external LDAP authentication

2011-04-27 Thread Leandro Hermida
Hi Pieter, On Wed, Apr 27, 2011 at 4:14 PM, Pieter Neerincx pieter.neeri...@gmail.comwrote: Hi Leandro, On Apr 27, 2011, at 3:50 PM, Leandro Hermida wrote: Hi, Just wondering if I got my setup right, I have Galaxy front-ended by Apache doing the static caching, proxying and LDAP auth

[galaxy-dev] anyone actually properly implemented remote_user_logout_href with external HTTP authentication?

2011-04-28 Thread Leandro Hermida
Hi everyone, Has anyone actually properly implemented remote_user_logout_href in Galaxy with external HTTP authentication? As probably those who have tried know, it is rife there doesn't seem to be a clean and robust way to do this? best, Leandro

Re: [galaxy-dev] Launching multiple jobs using one tool form with multiple selected datasets

2011-04-28 Thread Leandro Hermida
On Apr 27, 2011, at 9:40 AM, Leandro Hermida wrote: Hi Dannon, Thanks for your replies and advice, this leads me to a quesion... is it possible to execute a tool job via the Galaxy API just like someone does via the UI? Could I then have a tool script that wraps this programmatic execution

Re: [galaxy-dev] Getting tool dirpath in a Python code file

2011-04-28 Thread Leandro Hermida
Hi galaxy developers, Just want to double-check, there is no way to import some kind of galaxy tool context info into python code you are running for a tool? best, leandro On Fri, Apr 15, 2011 at 8:03 PM, Leandro Hermida soft...@leandrohermida.com wrote: On Fri, Apr 15, 2011 at 7:27 PM

[galaxy-dev] tool parameter attribute for option display value (not passed value)?

2011-04-28 Thread Leandro Hermida
Hi, For a tool select input parameter: param name=input1 type=select option value=hs33Homo sapiens/option option value=mm19Mus musculus/option option value=rn43Rattus norvegicus/option /param Is there an attribute for the variable $input1 that will give me the displayed value (e.g.

Re: [galaxy-dev] User Name not set with external LDAP authentication

2011-04-28 Thread Leandro Hermida
On Thu, Apr 28, 2011 at 5:33 PM, Nate Coraor n...@bx.psu.edu wrote: Pieter Neerincx wrote: Hi Leandro, On Apr 27, 2011, at 6:08 PM, Leandro Hermida wrote: Hi Pieter, cut I have this *exact* same setup as you where I am authenticating with the LDAP user ID and returning

Re: [galaxy-dev] anyone actually properly implemented remote_user_logout_href with external HTTP authentication?

2011-04-28 Thread Leandro Hermida
On Thu, Apr 28, 2011 at 5:52 PM, Nate Coraor n...@bx.psu.edu wrote: Leandro Hermida wrote: Hi everyone, Has anyone actually properly implemented remote_user_logout_href in Galaxy with external HTTP authentication? As probably those who have tried know, it is rife there doesn't seem

[galaxy-dev] param type=float optional=true doesn't work

2011-05-12 Thread Leandro Hermida
Hi, how do you make float parameter types fully optional? optional=true doesn't work. -Leandro ___ 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,

[galaxy-dev] select menu in conditional tag cannot be set at runtime in workflow editor

2011-05-13 Thread Leandro Hermida
Hi all, In a tool XML I have a select menu param within/driving a conditional tag and in the workflow editor it doesn't let me choose to allow the user to set this select menu at runtime? Is this a bug? best, leandro ___ Please keep all

[galaxy-dev] wait thread: 1002:Not enough memory. error after enabling DRMAA

2011-05-18 Thread Leandro Hermida
Hi all, I enabled DRMAA on my test Galaxy server installation and in the server startup output I get the following strange E #14ca [ 1.10] * wait thread: 1002:Not enough memory. lines after loading the job manager: ... galaxy.jobs.runners.local INFO 2011-05-18 17:10:23,025 starting workers

[galaxy-dev] Increase select multiple menu width for param tag type=data

2011-05-18 Thread Leandro Hermida
Hi, Is there a way to increase the width of a select multiple menu for a param tag type=data? Certain dataset labels I have are very informative :) (i.e. long) and when used as an input to a tool you can't read what the difference is between each item unless you look at the dataset number and

Re: [galaxy-dev] wait thread: 1002:Not enough memory. error after enabling DRMAA

2011-05-18 Thread Leandro Hermida
. I moved to the previous version and everything is OK for me Marina On 18/05/2011 16:15, Leandro Hermida wrote: Hi all, I enabled DRMAA on my test Galaxy server installation and in the server startup output I get the following strange E #14ca [ 1.10] * wait thread: 1002:Not enough

[galaxy-dev] nice quality Galaxy logo and name

2011-05-19 Thread Leandro Hermida
Hi there, Would anyone have a nice quality Galaxy logo and name image for presentations and posters? I've been using the one in the left hand corner of the server which ok but wondering if there is a better official one or something regards, leandro

Re: [galaxy-dev] issue with LSB_DEFAULTQUEUE

2011-05-19 Thread Leandro Hermida
configuration in universe_wsgi.ini default_cluster_job_runner = drmaa://-q srpipeline -P pipeline/ -q for the queue and -P for the project Marina On 19/05/2011 12:54, Leandro Hermida wrote: Hi Marina, Thank you so much for your help, LSF DRMAA is working fine with Galaxy now. One final problem

Re: [galaxy-dev] Specifying number of requested cores to Galaxy DRMAA

2011-05-19 Thread Leandro Hermida
your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ On 05/19/2011 12:03 PM, Leandro Hermida wrote: Hi, When Galaxy is configured to use the DRMAA job runner is there a way for a tool to tell DRMAA the number of cores it would like

Re: [galaxy-dev] wait thread: 1002:Not enough memory. error after enabling DRMAA

2011-05-19 Thread Leandro Hermida
, -- Message: 13 Date: Wed, 18 May 2011 17:15:06 +0200 From: Leandro Hermida soft...@leandrohermida.com To: Galaxy Dev galaxy-...@bx.psu.edu Subject: [galaxy-dev] wait thread: 1002:Not enough memory. error after enabling DRMAA Message-ID: BANLkTi=J4

[galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple=true input datasets

2011-05-19 Thread Leandro Hermida
Hi, I have a tool where the input is multi-select of datasets, e.g.: param type=data multiple=true name=input1 / I tested it to see what it would pass to my command and I get the following debug page and error in Galaxy: AttributeError: 'list' object has no attribute 'missing_meta' The last

Re: [galaxy-dev] Specifying number of requested cores to Galaxy DRMAA

2011-05-19 Thread Leandro Hermida
multithreaded tool, so it doesn't run a multithreaded job when there's only one core available in the chosen node. Hope that helps :) Regards, L-A On 05/19/2011 03:05 PM, Leandro Hermida wrote: Hi Louise-Amelie, Thank you for the post reference, this is exactly what I was looking

Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple=true input datasets

2011-05-19 Thread Leandro Hermida
in Galaxy just fine. I would like to use multiple of these output datasets in my history as the input for this other tool but something seems to be wrong if you try to do this? a bit lost, Leandro On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi, I have a tool

[galaxy-dev] select multiple tool input parameter bugs?

2011-05-19 Thread Leandro Hermida
I have the following tool input parameter: param name=columns type=select multiple=true label=Select which columns to output optionSIZE/option optionES/option option selected=trueNES/option optionNOM p-val/option option selected=trueFDR q-val/option optionFWER p-val/option

Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple=true input datasets

2011-05-19 Thread Leandro Hermida
format=html and this works and displays in Galaxy just fine. I would like to use multiple of these output datasets in my history as the input for this other tool but something seems to be wrong if you try to do this? a bit lost, Leandro On Thu, May 19, 2011 at 3:30 PM, Leandro Hermida soft

Re: [galaxy-dev] select multiple tool input parameter bugs?

2011-05-20 Thread Leandro Hermida
. best, Leandro On Thu, May 19, 2011 at 7:12 PM, Leandro Hermida soft...@leandrohermida.com wrote: I have the following tool input parameter: param name=columns type=select multiple=true label=Select which columns to output optionSIZE/option optionES/option option selected

Re: [galaxy-dev] Checkboxes/booleans in tools, again

2011-05-23 Thread Leandro Hermida
Not everything works correctly with checkbox booleans, the bug a couple people and I reported long ago https://bitbucket.org/galaxy/galaxy-central/issue/393/cant-use-checkbox-boolean-with-conditional is still there. 2011/5/23 Peter Cock p.j.a.c...@googlemail.com 2011/5/23 Louise-Amélie

Re: [galaxy-dev] nice quality Galaxy logo and name

2011-05-24 Thread Leandro Hermida
enough for some purposes, but will look much better than what you have been using. Sometime in the near future I hope to get a page like this http://gmod.org/wiki/GMOD_Promotion up for Galaxy. Thanks, Dave C. On Thu, May 19, 2011 at 12:15 PM, Leandro Hermida soft...@leandrohermida.com wrote

Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple=true input datasets

2011-05-24 Thread Leandro Hermida
have an answer for you, but when we're all back at work next week, someone should be able to respond. Thanks, --nate Leandro Hermida wrote: Hi again, Very sorry to ask again, just gotten no repsonse, but is this a Galaxy bug or does anyone have a functioning tool that takes multiple

Re: [galaxy-dev] galaxy download

2011-05-24 Thread Leandro Hermida
See this page for the official installation instructions https://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy 2011/5/24 Björn Grüning bjoern.gruen...@pharmazie.uni-freiburg.de Hi Jasmin, at first you need to install mercurial. Under debian/ubuntu install it with: sudo apt-get

[galaxy-dev] new galaxy-dist fixes multiple IE UI bugs

2011-05-25 Thread Leandro Hermida
Thanks Galaxy Dev Team, the new galaxy-dist fixes multiple UI bugs with IE, for e.g. the workflow editor works now works and the history expand/collapse works! :) ___ Please keep all replies on the list by using reply all in your mail client.

Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple=true input datasets

2011-06-09 Thread Leandro Hermida
, 2011 at 1:31 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi Nate, Thanks for the ping, have fun at the conference! On Tue, May 24, 2011 at 11:22 AM, Nate Coraor n...@bx.psu.edu wrote: Hi Leandro, The Galaxy Team has recently been preparing for and traveling in advance of the Galaxy

Re: [galaxy-dev] use external authentication bare username as email address without appending any email domain

2011-06-09 Thread Leandro Hermida
. thank a lot, Leandro On Thu, Jun 9, 2011 at 6:54 PM, Nate Coraor n...@bx.psu.edu wrote: Leandro Hermida wrote: Hi, Is it possible to tell Galaxy to use the bare username passed back by external authentication as the email address without appending any domain?  It seems to complain

Re: [galaxy-dev] use external authentication bare username as email address without appending any email domain

2011-06-10 Thread Leandro Hermida
, people's email addresses are their usernames and email services work in Windows as your username is your email nickname. -L On Thu, Jun 9, 2011 at 11:00 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi Nate, Thank so much for the instructions :) , yes this is what I would want to do

[galaxy-dev] change dataset label in exec_after_process()

2011-06-23 Thread Leandro Hermida
Hi everyone, Is it possible to change dataset labels in exec_after_process() ? best, Leandro ___ 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,

[galaxy-dev] error when using exec_before_job

2011-06-23 Thread Leandro Hermida
Hi, I've tried to do a simple test where I change the output dataset name programmatically before it appears in the history using exec_before_job(). I just copied some example code: def exec_before_job(inp_data, out_data, param_dict, tool): for name, data in out_data.items():

Re: [galaxy-dev] change dataset label in exec_after_process()

2011-06-24 Thread Leandro Hermida
success setting dataset label/name and other attributes using one of the custom code hook functions?? thanks, leandro On Thu, Jun 23, 2011 at 3:27 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi everyone, Is it possible to change dataset labels in exec_after_process() ? best, Leandro

Re: [galaxy-dev] change dataset label in exec_after_process()

2011-06-24 Thread Leandro Hermida
format=html name=html_file label=${out_prefix}.html/ /outputs works for me and avoids the need to have a post execution hook code file. On Fri, Jun 24, 2011 at 6:02 PM, Leandro Hermida soft...@leandrohermida.com wrote: Hi again, Sorry that I didn't know before, it seems like the label

[galaxy-dev] updating ToolsMultipleOutput wiki docs new additional datasets file format to include database part

2011-06-24 Thread Leandro Hermida
Hi, In the last section of https://bitbucket.org/galaxy/galaxy-central/wiki/ToolsMultipleOutput, Number of output datasets cannot be determined until tool run, it should be updated that the new additional datasets file format actually has a sixth part at the end where you can set the database

Re: [galaxy-dev] public datasets/histories with external auth

2011-06-29 Thread Leandro Hermida
Hi Shantanu, In your Apache configuration exactly how did you set up an anonymous REMOTE_USER just for specific locations like the /datasets/ path? I'm just looking at the Apache docs and the RequestHeader directive has a context of the entire VirtualHost and cannot be put into a Location

Re: [galaxy-dev] public datasets/histories with external auth

2011-06-30 Thread Leandro Hermida
Hi Nate and Shantanu, Thanks so much for the clear guidance, this works and sorry I didn't read the Apache docs properly best, Leandro On Thu, Jun 30, 2011 at 6:14 AM, Shantanu Pavgi pa...@uab.edu wrote: On Jun 29, 2011, at 12:21 PM, Nate Coraor wrote: Leandro Hermida wrote: Hi Shantanu

Re: [galaxy-dev] AttributeError: 'list' object has no attribute 'missing_meta' when doing multiple=true input datasets

2011-07-01 Thread Leandro Hermida
  return value.id AttributeError: 'list' object has no attribute 'id' Is using multiple history items as a single input not currently supported, or is there something else I'm doing wrong? Cheers, Kip On Thu, Jun 9, 2011 at 7:05 AM, Leandro Hermida soft...@leandrohermida.com wrote: Hi

[galaxy-dev] Galaxy forgetting history and giving me new blank history

2011-07-01 Thread Leandro Hermida
Having a very strange problem in the Galaxy web GUI that suddenly just started happening yesterday, getting very strange behavior in the history right panel. - Most of the time when I click on something in the GUI like to go to a tool page or to go to the Admin interface and come back suddenly

Re: [galaxy-dev] public datasets/histories with external auth

2011-07-01 Thread Leandro Hermida
/galaxy_dist/static/robots.txt [L] RewriteRule ^(.*) http://galaxy.server.hostname:8080 [P] On Fri, Jul 1, 2011 at 12:13 AM, Shantanu Pavgi pa...@uab.edu wrote: On Jun 30, 2011, at 6:34 AM, Leandro Hermida wrote: Hi Nate and Shantanu, Thanks so much for the clear guidance, this works

Re: [galaxy-dev] public datasets/histories with external auth

2011-07-01 Thread Leandro Hermida
1, 2011 at 10:36 AM, Leandro Hermida soft...@leandrohermida.com wrote: Hi Shantanu, Thank you for your update, I've done my config a little differently and it appears to work just the same. The relevant part looks like this: Location / ## ActiveDirectory authentication

Re: [galaxy-dev] Galaxy forgetting history and giving me new blank history

2011-07-01 Thread Leandro Hermida
Hi - you can ignore this message, I figured out what the problem was and it was caused by a change in my front end authentication setup On Fri, Jul 1, 2011 at 10:21 AM, Leandro Hermida soft...@leandrohermida.com wrote: Having a very strange problem in the Galaxy web GUI that suddenly just

[galaxy-dev] value_label tool input param attribute doesn't work as documented

2011-07-14 Thread Leandro Hermida
Hi, Looking at the example on the Tool Config Syntax wiki page: Example Assume that the tool includes an input parameter named database which is a select list ( e.g., assume the following inputs ): Toggle line numbershttp://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax# 1

[galaxy-dev] problems with two coupled select menus using dynamic_options and refresh_on_change

2011-07-27 Thread Leandro Hermida
Hi, I am trying to create a form where there are two select menus, both using dynamic_options, where one is the parent menu that is chosen first and based on the selection(s) there is a refresh and the second menu gets populated based on the first menu's choice(s). param name=names type=select

Re: [galaxy-dev] value_label tool input param attribute doesn't work as documented

2011-09-07 Thread Leandro Hermida
this on my instance and the example you gave did give me the correct string: Human (hg18). Do you still have this problem? If so, can you provide an example where it still behaves incorrectly? Thanks, K On Thu, Jul 14, 2011 at 4:16 AM, Leandro Hermida soft...@leandrohermida.com wrote: Hi

[galaxy-dev] uploading binary files checksum changes, Galaxy doing something to file?

2011-09-16 Thread Leandro Hermida
Hi all, We tried to find something in the docs and mailing list no luck. We created a new datatype the is a straight subclass of Binary and then when we upload such a file in the Galaxy UI and check the checksums between the original file and the file located in the Galaxy database/files/...

[galaxy-dev] Galaxy Tool Shed used for main code hosting and collaborative development repo?

2011-11-15 Thread Leandro Hermida
Hi, Quick question about the Galaxy Tool Shed, I would like to publish a tool suite there and wondering to people use the tool shed repositories as their main code hosting and development site or is it typical that people have their code hosted somewhere else a la Github or Sourceforge? regards,

[galaxy-dev] .gz extension gets stripped off when uploading via data library Upload via filesystem paths but not via Get Data - Upload File

2012-01-20 Thread Leandro Hermida
Hello, We've created a new binary datatype for .fastq.gz files following the same methodology as the BAM files since we don't want our fasta.gz files to be gunzipped. I added the appropriate code in upload.py to make sure of this. This new datatype and extension successfully does not gunzip our

Re: [galaxy-dev] .gz extension gets stripped off when uploading via data library Upload via filesystem paths but not via Get Data - Upload File

2012-01-20 Thread Leandro Hermida
by specifying its own new datatype and extension and changing binary.py to make sure it doesn't fall through to the elsif where it tries to unzip stuff. On Fri, Jan 20, 2012 at 2:25 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Jan 20, 2012 at 12:42 PM, Leandro Hermida soft

Re: [galaxy-dev] .gz extension gets stripped off when uploading via data library Upload via filesystem paths but not via Get Data - Upload File

2012-01-20 Thread Leandro Hermida
.             uploaded_dataset.data.dataset.purgable = False             trans.sa_session.add_all( ( uploaded_dataset.data, uploaded_dataset.data.dataset ) )             trans.sa_session.flush()         return uploaded_dataset Thanks! Greg On Jan 20, 2012, at 7:42 AM, Leandro Hermida wrote: Hello, We've created a new binary datatype

[galaxy-dev] problem with Input dataset workflow control feature and custom non-subclass datatypes

2012-01-20 Thread Leandro Hermida
Hi, There seems to be a weird bug with the Input dataset workflow control feature, hard to explain clearly but I'll try my best. If you define a custom datatype that is a simple subclass of an existing galaxy datatype, e.g.: datatype extension=myext type=galaxy.datatypes.data:Text subclass=True

[galaxy-dev] Problem running purge_datasets.sh cleanup scripts

2012-01-25 Thread Leandro Hermida
Hello, In the latest galaxy-dist version when running the system cleanup commands in the documented order I get an error when running the purge_datasets.sh script: sh delete_userless_histories.sh sh purge_histories.sh sh purge_libraries.sh sh purge_folders.sh sh delete_datasets.sh sh

Re: [galaxy-dev] problem with Input dataset workflow control feature and custom non-subclass datatypes

2012-01-25 Thread Leandro Hermida
. -Dannon On Jan 20, 2012, at 11:07 AM, Leandro Hermida wrote: Hi, There seems to be a weird bug with the Input dataset workflow control feature, hard to explain clearly but I'll try my best. If you define a custom datatype that is a simple subclass of an existing galaxy datatype

[galaxy-dev] input param with type=data multiple=true working?

2012-01-26 Thread Leandro Hermida
Hello, There have been previous requests/questions (some mine) about fixing Galaxy tool functionality to enable a multiple select menu item for input data in the history with the following: param ... type=data multiple=true ... / Instead of using the cumbersome repeat tags and resulting form.

[galaxy-dev] Tool syntax to embed external web page doesn't quite work as desired anymore

2012-02-06 Thread Leandro Hermida
Hi everyone, It used to be in the previous or so galaxy-dist that if you wanted to have a tool which displayed a web page from another web app in the center Galaxy frame you simply did: tool name=View External Web Page id=view_external_page version=1.0.0 descriptionfrom External

[galaxy-dev] Illumina HiSeq 2000 external service type XML

2012-02-21 Thread Leandro Hermida
Hi everyone, Does anyone have a typical external service type XML file for an Illumina HiSeq 2000? I have created one but not sure if its correct and there is no guide for creating the external service type XMLs thanks, Leandros ___ Please

Re: [galaxy-dev] uploads stuck in history

2012-02-22 Thread Leandro Hermida
Hi all, We get the behavior mentioned some times too, its not reproducible just like you mentioned. Some times it happens with small files, some times with large files and again as you said it doesn't happen all the time. Now I haven't seen this yet on our Galaxy dev server which is the latest

[galaxy-dev] can the sample tracking system transfer (copy) data to a dataset library not in private Galaxy server data directory tree and then just link files?

2012-02-27 Thread Leandro Hermida
Dear all, Is there a way with the Galaxy sample tracking system to have the dataset transfer feature copy data to a dataset library outside the private Galaxy server data directory tree and then the dataset library just link (like you can do with upload files feature when managing data

[galaxy-dev] refresh_on_change is broken?

2012-02-29 Thread Leandro Hermida
Hello, Seems like the refresh_on_change functionality is broken in the latest galaxy-dist. If you apply it to an input parameter it doesn't seem to refresh the page when you change the selection of that parameter. Does anyone else also have the problem? regards, Leandro

[galaxy-dev] bug with Galaxy form validation and dynamic_options population of drop-down menus where option values are integers

2012-02-29 Thread Leandro Hermida
Hello, If you have a form with an input like this: param name=input1 type=select dynamic_options=get_options() / And the options dynamically generated have integers as values, e.g. options tuples like this: [ One, 1, 1 ], [ Two, 2, 0 ], [ Three, 3, 0 ] When you try to submit the galaxy form

Re: [galaxy-dev] bug with Galaxy form validation and dynamic_options population of drop-down menus where option values are integers

2012-03-01 Thread Leandro Hermida
],      [ Three,3,False]                          work? Regards, Hans On 02/29/2012 04:44 PM, Leandro Hermida wrote: Hello, If you have a form with an input like this: param name=input1 type=select dynamic_options=get_options() / And the options dynamically generated have integers as values, e.g

Re: [galaxy-dev] uploads stuck in history

2012-03-08 Thread Leandro Hermida
Hello, We don't use the nginx module kind regards, Leandro On Wed, Mar 7, 2012 at 4:42 PM, Jorrit Boekel jorrit.boe...@scilifelab.se wrote: Hi Nate, I wasn't before, but I switched to nginx now. Non-uploading is still happening in firefox (10.0.2 on ubuntu 11.10). I can't be 100% sure

Re: [galaxy-dev] bug with Galaxy form validation and dynamic_options population of drop-down menus where option values are integers

2012-03-13 Thread Leandro Hermida
, Leandro Hermida wrote: Hello, If you have a form with an input like this: param name=input1 type=select dynamic_options=get_options() / And the options dynamically generated have integers as values, e.g. options tuples like this: [ One, 1, 1 ], [ Two, 2, 0 ], [ Three, 3, 0 ] When you try

Re: [galaxy-dev] refresh_on_change is broken?

2012-03-20 Thread Leandro Hermida
, seems like you are using jQuery to bind a custom Javascript refresh_on_change function but when you look at that function it doesn't do any form reloading, maybe just the feature is unfinished? sincerely, Leandro On Wed, Feb 29, 2012 at 10:34 AM, Leandro Hermida soft...@leandrohermida.com wrote

Re: [galaxy-dev] refresh_on_change is broken?

2012-03-21 Thread Leandro Hermida
? *Can you be more specific about what problems you're seeing and whether you can reproduce with known tools? Thanks, J. On Mar 20, 2012, at 9:28 AM, Leandro Hermida wrote: Hi everyone, Sorry to ping again, having the refresh_on_change functionality not working in Galaxy has us making

Re: [galaxy-dev] refresh_on_change is broken?

2012-03-21 Thread Leandro Hermida
? *Can you be more specific about what problems you're seeing and whether you can reproduce with known tools? Thanks, J. On Mar 20, 2012, at 9:28 AM, Leandro Hermida wrote: Hi everyone, Sorry to ping again, having the refresh_on_change functionality not working in Galaxy has us making

Re: [galaxy-dev] refresh_on_change is broken?

2012-03-22 Thread Leandro Hermida
in the second menu can be re-executed using the new file name as a parameter then generating new options in this second menu? regards, Leandro On Mar 21, 2012, at 9:27 AM, Leandro Hermida wrote: Here's one example: inputs    param type=data name=dataset refresh_on_change=true label=Select a file

[galaxy-dev] Galaxy AMQP listener startup script error

2012-03-23 Thread Leandro Hermida
Dear all, I followed the directions in https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer to set up the Galaxy AMQP listener service so that the sample tracking system can transfer datasets. When running nohup sh run_galaxy_listener.sh Traceback (most recent call last): File

[galaxy-dev] New Galaxy look from usegalaxy.org

2012-03-26 Thread Leandro Hermida
Dear all, How do I get the new Galaxy look enabled that you see in usegalaxy.org? I have two servers on the latest galaxy-dist. regards, Leandro ___ Please keep all replies on the list by using reply all in your mail client. To manage your

[galaxy-dev] Normal that latest galaxy-dist creates shed_tools directory one level up from the galaxy-dist directory?

2012-03-26 Thread Leandro Hermida
Dear all, Is it normal that the latest galaxy-dist creates a shed_tools directory one directory up (and outside) from the server galaxy-dist directory? best, Leandro ___ Please keep all replies on the list by using reply all in your mail

[galaxy-dev] Sample tracking data transfer hangs in queue forever

2012-03-26 Thread Leandro Hermida
Dear Galaxy Dev, I've set up the Galaxy sample tracking system data transfer functionality exactly as specified here https://main.g2.bx.psu.edu/u/rkchak/p/data-transfer, but when I attempt to transfer datasets it puts them into the queue and then never seems to transfer anything. The

Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever

2012-03-28 Thread Leandro Hermida
it is either malformed or otherwise incorrect. Malformed LibraryFolder id ( 994debf9f6ab02b99d7cff57c04c6b7c ) specified, unable to decode What could be the problem here? Any help would be appreciated. regards, Leandro On Wed, Mar 28, 2012 at 1:15 PM, Leandro Hermida soft...@leandrohermida.com wrote: Dear

Re: [galaxy-dev] Sample tracking data transfer hangs in queue forever

2012-03-28 Thread Leandro Hermida
version from last year and everything works ok during library folder association. regards, Leandro On Wed, Mar 28, 2012 at 1:20 PM, Leandro Hermida soft...@leandrohermida.com wrote: Dear Galaxy Dev, Now I have another problem with the Galaxy sample tracking data transfer.  Galaxy is not able

[galaxy-dev] AttributeError: 'NoneType' object has no attribute 'decode' with Dataset Actions -- Select more datasets

2012-03-28 Thread Leandro Hermida
Dear Galaxy Dev, On the viewed transferred datasets screen, when you click on Dataset Actions -- Select more datasets, I get the following error and stack trace: AttributeError: 'NoneType' object has no attribute 'decode' URL:

[galaxy-dev] Setting genome build on datasets transferred from sample tracking external service

2012-03-30 Thread Leandro Hermida
Dear Galaxy Dev, Is there a way to set the genome build metadata on datasets transferred from an external service in the sample tracking system? -Leandro ___ Please keep all replies on the list by using reply all in your mail client. To

Re: [galaxy-dev] problem with ~/lib/galaxy/app.py after code upgrade to March 12, 2012 release ('6799:40f1816d6857')

2012-04-24 Thread Leandro Hermida
Dear Hans, //galaxy_dist/eggs/sqlalchemy_migrate-0.5.4-py2.6.egg/migrate/versioning/schema.py, line 42, in _load data = list(result)[0] IndexError: list index out of range This error is because SQLAlchemy cannot load the controlled schema version info from the DB, the result is empty, so