Re: [galaxy-dev] megablast and blastdb

2011-02-15 Thread Bossers, Alex
David, this is what we have in blastdb.loc (nucleotide) or blastdb_p.loc (prot)a snippettab delimited caption can contain spaces so I increased the tab for display only #This is a sample file distributed with Galaxy that is used to define a #list of nucleotide BLAST databases, using

[galaxy-dev] percent and pipe sign in text input fields

2011-02-16 Thread Bossers, Alex
Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or %f it returns Xf or Xf in the the variable. For

[galaxy-dev] Percent and pipe sign in text input fields

2011-02-16 Thread Bossers, Alex
Hello all, I have a tool based on blastdbcmd that contains a param tag of type text. I want to be able to use the % sign in that text field users can enter (%g is for instance the field identifier for gi). However, if I do for instance %f or %f it returns Xf or Xf in the the variable. For

Re: [galaxy-dev] Percent and pipe sign in text input fields

2011-02-16 Thread Bossers, Alex
...@gmail.com] Verzonden: woensdag 16 februari 2011 15:44 Aan: Bossers, Alex CC: galaxy-...@bx.psu.edu Onderwerp: Re: [galaxy-dev] Percent and pipe sign in text input fields Hi Alex, Galaxy sanitizes the params to remove unsafe characters. It's a security feature. From a previous post some time

Re: [galaxy-dev] Percent and pipe sign in text input fields

2011-02-16 Thread Bossers, Alex
...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] namens Bossers, Alex [alex.boss...@wur.nl] Verzonden: woensdag 16 februari 2011 16:33 Aan: galaxy-...@bx.psu.edu Onderwerp: Re: [galaxy-dev] Percent and pipe sign in text input fields Daniel/Pieter, thanks for the hints. I solved it using

Re: [galaxy-dev] listing the same tool twice in tool_conf.xml

2011-02-21 Thread Bossers, Alex
Branden, we have also customised the tol menu and added a university specific section on top just beneath Get data. We have also listed tools twice for convenience. I do not see the need t list a tool twice in the same expanding section. But in another section it should work flawlessly. Having

[galaxy-dev] DB access and passowrd field

2011-03-19 Thread Bossers, Alex
Hi All, I have some tools that generate some tabular output. The next step is to aggregate the data for some filtering and analysis. In my view the best way to do by using a DB (MySQL in my case). Tools and cmd line wrappers can easily connect to this DB (another database than galaxy is using

Re: [galaxy-dev] DB access and password field in galaxy

2011-03-30 Thread Bossers, Alex
Hello all, Maybe I posted it wrong. But below my original message again. Any ideas? Thanks Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: zaterdag 19 maart 2011 10:23 Aan: galaxy-dev

Re: [galaxy-dev] DB access and password field in galaxy

2011-03-30 Thread Bossers, Alex
] Verzonden: woensdag 30 maart 2011 17:11 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] DB access and password field in galaxy Hello Alex, We have a similar setup, and this is how we implemented it: 1. all users must be logged in, so $userEmail is set to the correct

Re: [galaxy-dev] Using a Galaxy image on a local system

2011-04-28 Thread Bossers, Alex
Clare, The NBIC bioassist consortium has a ready to run galaxy VM available as well. Its here: https://wiki.nbic.nl/index.php/Galaxy_VM also via bitorrent. It's sort of mirror of the public nbic instance. Good luck, Alex Van: galaxy-dev-boun...@lists.bx.psu.edu

Re: [galaxy-dev] A tool with no inputs

2011-05-16 Thread Bossers, Alex
Yes, as referred to by Peter we solved this by having a single radio-button and some dummy text. If you just have a single radio it doesn't show up and only displays the text. So it basically just gives me the execute button. Snippet attached below; We used it for a tool that refreshes some

Re: [galaxy-dev] Need help with uploading a perl script in Galaxy local instance

2011-05-23 Thread Bossers, Alex
Indeed looking at the script it should be possible to use it as Vipin indicated. However, for xml validity I wouldn't use the 'naked' or signs but use gt; instead. I am curious though on the script. Is it part of a larger script? Don't see any ARGs being read from command line but

Re: [galaxy-dev] Need help with uploading a perl script in Galaxy local instance

2011-05-23 Thread Bossers, Alex
Ah right. Overlooked the shortcut EMPTY Just not my way of doing it.. Alex Van: Vipin TS [vipin...@gmail.com] Verzonden: maandag 23 mei 2011 17:39 Aan: Bossers, Alex CC: Jayant Khopale; galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Need help

Re: [galaxy-dev] Problem fore getting tool Command in code file

2011-05-24 Thread Bossers, Alex
Shashi, I guess you are looking for the tool configuration XML options? https://bitbucket.org/galaxy/galaxy-central/wiki/ToolConfigSyntax I guess its needless to say that you can only do this on your own instance of galaxy locally. Alex Van: galaxy-dev-boun...@lists.bx.psu.edu

Re: [galaxy-dev] stdout and stderr

2011-05-26 Thread Bossers, Alex
Alternatively you can redirect your STDOUT and/or STDERR into a LOG txt file as additional output to the tool. I do many times the same since it allows the realtime tracking in the log file of the process where it is and when it's expected to be finished. Indeed a wrapper can be used but if you

Re: [galaxy-dev] stdout and stderr

2011-05-26 Thread Bossers, Alex
PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT and STDOUT to a logfile. You won't get a red box though when errors occur! Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: donderdag 26 mei 2011 15

Re: [galaxy-dev] stdout and stderr

2011-05-26 Thread Bossers, Alex
, Alex CC: shashi shekhar; galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] stdout and stderr On Thu, May 26, 2011 at 2:42 PM, Bossers, Alex alex.boss...@wur.nl wrote: PS: 2 is STDERR and 1 is STDOUT. One could do a redirect of STDERR to STDOUT and STDOUT to a logfile. You won’t get a red box

Re: [galaxy-dev] Implemented adding tools via admin console

2011-05-30 Thread Bossers, Alex
Peter, if you were just interested in having a dynamic refresh it was posted long time ago and we have it operational. It comes as a tool in your tool list and refreshes all from the tool_conf.xml. Not the loc filtes though! As far as i remember it doesn't kill running jobs. It requires two

[galaxy-dev] MUMmer and TopHit filter

2011-05-31 Thread Bossers, Alex
Our first tools arrived at the toolshed; The MUMmer genome comparison suite and a TopHit filter. Enjoy and we appreciate any feedback for improvement: http://community.g2.bx.psu.edu/tool/browse_tools?operation=tools_by_categoryid=062d90505b2e763dwebapp=community Alex

[galaxy-dev] Launching a JAVA or external app

2011-06-27 Thread Bossers, Alex
Hello all, would it be possible to launch for instance a JAVA app with preloaded parameters and files from galaxy that needs interaction/display? For instance a gui based annotation editor? It necessarily doesn't have to support saving of files back to galaxy. Sort of end stage. Any help or

Re: [galaxy-dev] Refreshing/Reloading Files

2011-06-29 Thread Bossers, Alex
Paul, as far as I know the config files (probably loc files) are only refreshed on galaxy_instance restart unfortunatly. So when this is possible to do on the fly I am interested as well. Alex Van: galaxy-dev-boun...@lists.bx.psu.edu

[galaxy-dev] Hidden history item

2011-07-06 Thread Bossers, Alex
Hi all, by default I let my tools produce (the old way) a logfile of the console and additional running statistics. This is convenient at tool setup and ocassionally for troubleshooting. Anyway I would like to make the corresponding history item hidden. I tried including hidden=true in the

[galaxy-dev] bug or feature :)

2011-07-06 Thread Bossers, Alex
In our local instance (central version) up to changeset (June 28th) I noticed in the admin panel to manage jobs some odd behaviour; When I set the update Jobs cutoff on 10 seconds and press refresh the item below (administrative Job Lock) is also activated and new jobs are locked. Is that a

[galaxy-dev] Error moving tool-data dir ... bowite indexes missing

2011-07-22 Thread Bossers, Alex
On our up-to-date galaxy_central version I have successfully moved the database/files directory to mounted storage. After adapting the universe_wsgi.ini it works fine after galaxy restart. Now the tool-data dir becomes bigger and bigger and I wanted to move that to mounted storage as well. I

Re: [galaxy-dev] Error moving tool-data dir ... bowite indexes missing

2011-07-22 Thread Bossers, Alex
Mus_musculus.NCBIM37Mus musculus NCBIM37 /share/bowtie/indexes/Mus_musculus.NCBIM37 Mouse -- -Oorspronkelijk bericht- Van: Ross [mailto:ross.laza...@gmail.com] Verzonden: vrijdag 22 juli 2011 15:15 Aan: Bossers, Alex Onderwerp: Re: [galaxy-dev] Error moving tool-data dir

Re: [galaxy-dev] Does Galaxy have a tool to run R script?

2011-07-31 Thread Bossers, Alex
You can also directly link the R script in the galaxy-tool. We have many of those. For testing (NOT SAFE!) we also have a tool that allows the upload of an R script for testing purposes See the arhives for more extensive discussion... command R --slave --vanilla

Re: [galaxy-dev] filter

2011-08-04 Thread Bossers, Alex
If I understand it correctly; You have to check the sanitize option for your tool. The pipe (among others) is usually by default sanitised into X. Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens KOH Jia Yu Jayce Verzonden: donderdag 4 augustus

Re: [galaxy-dev] filter

2011-08-15 Thread Bossers, Alex
, Alex CC: 'galaxy-dev@lists.bx.psu.edu' Onderwerp: RE: filter Hi thanks, but what sanitizer option should I set it to? -Original Message- From: Bossers, Alex [mailto:alex.boss...@wur.nl] Sent: Thursday, August 04, 2011 3:11 PM To: KOH Jia Yu Jayce Cc: 'galaxy-dev@lists.bx.psu.edu' Subject

[galaxy-dev] odd behaviour of files from data libraries

2011-10-05 Thread Bossers, Alex
Since some time we are observing strange things happening to using files from our local data libraries in our local galaxy-central instance: The files and hierarchy stay there but when copied to the history. they turn up as being deleted and can only be used by selecting the view_deleted

Re: [galaxy-dev] HOW TO RETRIEVE DATA FROM HISTORY??!!

2011-10-20 Thread Bossers, Alex
Shaun, we took this quite easily by a simple tool we added to the toolbox. Just use the xml below as a new tool and you can get file paths of any file you like. Hope it helps, Alex tool id=filelocator name=Locate Data in Galaxy Database version=1.0.1 description/description commandecho

Re: [galaxy-dev] tool for RepeatMasker?

2011-11-27 Thread Bossers, Alex
The blast+ wrappers have DUST capability ON by default -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Smithies, Russell Verzonden: maandag 28 november 2011 1:27 Aan: 'Björn Grüning' CC:

Re: [galaxy-dev] Configure Tools/Blast

2011-12-04 Thread Bossers, Alex
There is some documentation on the wiki. You need to modify the designated .loc file. It has explained here on a BioStar qustion: http://biostar.stackexchange.com/questions/15035/custom-blast-db-on-galaxy-server Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu

[galaxy-dev] Toolshed fasta-section down?

2011-12-08 Thread Bossers, Alex
Hi The fasta-manipulation section on toolshed seems to be down (http://toolshed.g2.bx.psu.edu/). Am I the only one experiencing this? IE just returns me a blank error page not found. FF returns me another unhelpful error: Server Error An error occurred. See the error logs for

Re: [galaxy-dev] Automatic citation list from a tool, workflow, or history

2011-12-15 Thread Bossers, Alex
+1 for me :-) Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] namens Casey Bergman [casey.berg...@manchester.ac.uk] Verzonden: donderdag 15 december 2011 20:10 Aan: Peter Cock; Sean Davis CC: galaxy-dev@lists.bx.psu.edu

Re: [galaxy-dev] Hidden history item

2011-12-19 Thread Bossers, Alex
@lists.bx.psu.edu; Bossers, Alex Onderwerp: re: Hidden history item Alex, I just implemented this functionality in galaxy-central changset 303741fda0ec and documented it on the wiki. https://bitbucket.org/galaxy/galaxy-central/changeset/303741fda0ec http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config

Re: [galaxy-dev] Share some code (xml) to wrap IGV itself as a Galaxy visualizer

2012-01-17 Thread Bossers, Alex
Dan, any idea when the next dist release is scheduled? We need to upgrade our wur instance seriously and from then keep up the pace, but it would be a pity if we upgrade and extensively test it now, while the new release is out a few days later. The latest is from November 18th right?! Thanks

[galaxy-dev] How to delete user (and unshared files) in local instance by galaxy-admin (panel)

2012-01-27 Thread Bossers, Alex
Hi All, We are finally up-and-running again with the latest dist release. The previoous version was ok but already quite old. For our local public server at wur we are now encountering the awaited disk space issues. as had to come some daybut sooner anyway... So we have been cleaning

Re: [galaxy-dev] How to delete user (and unshared files) in local instance by galaxy-admin (panel)

2012-01-28 Thread Bossers, Alex
Van: Hans-Rudolf Hotz [h...@fmi.ch] Verzonden: zaterdag 28 januari 2012 13:10 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] How to delete user (and unshared files) in local instance by galaxy-admin (panel) Hi Alex Since

Re: [galaxy-dev] How to delete user (and unshared files) in local instance by galaxy-admin (panel)

2012-01-29 Thread Bossers, Alex
Greg, Thanks. Stupid to have missed that universe setting Alex Van: Greg Von Kuster [mailto:g...@bx.psu.edu] Verzonden: zaterdag 28 januari 2012 16:26 Aan: Bossers, Alex CC: Hans-Rudolf Hotz; galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] How to delete user (and unshared files

[galaxy-dev] Disk size of all users?

2012-01-29 Thread Bossers, Alex
Reading this on the wiki: http://wiki.g2.bx.psu.edu/Admin/Disk%20Quotas Shows that there is a record in the DB tracking the users allocated diskspace for histories. Is there a convenient way to get this info using the galaxy admin panels? Thereby we can track heavy users and urge them to

Re: [galaxy-dev] Disk size of all users?

2012-01-30 Thread Bossers, Alex
PS: This only seems to be true when disk quotas are in place. So where to get the per user disk usage? -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 30 januari 2012 8:56 Aan

Re: [galaxy-dev] How to delete user (and unshared files) in local instance by galaxy-admin (panel)

2012-01-30 Thread Bossers, Alex
: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] How to delete user (and unshared files) in local instance by galaxy-admin (panel) On Jan 27, 2012, at 4:43 PM, Bossers, Alex wrote: Hi All, We are finally up-and-running again with the latest dist release

[galaxy-dev] toolsectionlabel error (problem configuring toolshed hotplug?)

2012-02-03 Thread Bossers, Alex
Somehow I seem to miss something when configuring our latest up-to-date galaxy_central version to use the galaxy toolshed. When as admin I want to install a tool I can browse the given 2 repositories and select view tools. When I select install to local galaxy it drops an error on 2 tools I

Re: [galaxy-dev] Problem fetching updates to toolshed tool

2012-02-05 Thread Bossers, Alex
Hi Greg, Ok I pulled the latest changeset and updated the database. No probs. Now I am able to get tools from the galaxy main toolshed. Tested the table2html tool to be sure about no additional dependencies. It came up nicely with the section list I can install a tool to; but... I created an

Re: [galaxy-dev] Problem fetching updates to toolshed tool

2012-02-06 Thread Bossers, Alex
PS: when I make the section empty again in the original tool_conf.xml it doesn't show up anymore in that section. :-( Actually the complete section is again invisible. Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: maandag 6

Re: [galaxy-dev] Problem fetching updates to toolshed tool

2012-02-06 Thread Bossers, Alex
tested it with an empty section AND an empty shed_tool_conf thoughwill try to later...when I figured out how to completely remove a tool from the system. Thanks for the quick fix! Alex Van: Greg Von Kuster [mailto:g...@bx.psu.edu] Verzonden: maandag 6 februari 2012 16:21 Aan: Bossers, Alex CC

[galaxy-dev] history box odd behaviour

2012-02-13 Thread Bossers, Alex
Hi All, Since some of the last updates (I guess, since I didn't notice it before) I notice some odd behaviour of the history box when for instance doing BLAST searches on our local galaxy_central (latest version). When I run blastx as output xml it starts running fine (yellow box). I can start

Re: [galaxy-dev] history box odd behaviour

2012-02-13 Thread Bossers, Alex
Ok. Just filed a bug report. Alex -Oorspronkelijk bericht- Van: Langhorst, Brad [mailto:langho...@neb.com] Verzonden: maandag 13 februari 2012 17:38 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] history box odd behaviour On Feb 13, 2012, at 11:22 AM

Re: [galaxy-dev] uploads stuck in history

2012-02-23 Thread Bossers, Alex
I confirm the same strange behaviour since some of the last updates on the central version. We are at the latest now. It is also with medium (10Mb+ tarballs) AND large files! Furthermore its seems to be in FireFox only They upload fine using IE8 or 9. Didn't test other browsers though.

Re: [galaxy-dev] uploads stuck in history

2012-03-08 Thread Bossers, Alex
and not complaining. Is there any way to verify uploads are processed through nginx? jorrit On 03/05/2012 08:37 PM, Nate Coraor wrote: By any chance, do you all happen to be using the nginx upload module?   I am guessing not. --nate On Feb 23, 2012, at 3:16 AM, Bossers, Alex wrote: I confirm

[galaxy-dev] refresh loc files without restart

2012-03-08 Thread Bossers, Alex
Early 2011 there was a discussion and feature request to be able to refresh loc files on a running galaxy instance. This is not only convenient for updating loc files for blast, bowtie, bwa and such, but also opens possibilities to update and dynamically populate such files to be used in other

Re: [galaxy-dev] Local display application questions

2012-04-02 Thread Bossers, Alex
As an alternative you can return hidden history items. Not exactly what you want perhaps... Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] namens Peter Cock [p.j.a.c...@googlemail.com] Verzonden: maandag 2 april 2012 15:38

Re: [galaxy-dev] upload from local filesysem

2012-05-23 Thread Bossers, Alex
You can do so / allowing them to, by using the galaxy ftp solution. That way users can link or provide files in their email subdirs. You have to sort out how to set the users/rights properly on your linux box though. But see the galaxy ftp solution pages, it might be of help. Alex

Re: [galaxy-dev] scripts in welcome.html?

2012-06-15 Thread Bossers, Alex
You mean the javascript works right? Or did you manage to get the PHP inside? Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Smithies, Russell Verzonden: donderdag 14 juni 2012 1:45 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev]

Re: [galaxy-dev] Setting up proftpd problem: ftp login failure

2012-07-13 Thread Bossers, Alex
Joachim, If I remember correctly for our galaxy proftpd setup on ubuntu 10.10. Be sure to compile proftpd with the required additional SQL modules. Then figure out the user and group ids of galaxy user that can access the DB (mysql in our case). $ id galaxy (or whatever user you use) Make sure

[galaxy-dev] samtools pileup deprecated

2012-07-20 Thread Bossers, Alex
Hi All, Maybe I missed it on the list here, but it seems that for samtools the pileup command has been deprecated without backward compatibility from the more recent samtools packages... http://massgenomics.org/2012/03/5-things-to-know-about-samtools-mpileup.html Did anyone rewrite some of the

Re: [galaxy-dev] samtools pileup deprecated

2012-07-20 Thread Bossers, Alex
pileup command cmd = 'samtools mpileup %s -f %s %s %s' try: Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: vrijdag 20 juli 2012 12:20 Aan: 'galaxy-dev@lists.bx.psu.edu' Onderwerp: [galaxy-dev] samtools pileup

[galaxy-dev] History import returns size zero

2012-10-05 Thread Bossers, Alex
Dear all, I might have missed it on the list and cannot find it in the archive; When we import a history exported from the same or another galaxy instance it imports ok and all files are there and usuable, only the history size is 0. We are up to latest galaxy-central of October 4th. Is this a

[galaxy-dev] Instant crash on large history export

2012-10-05 Thread Bossers, Alex
Another problem; On our ubuntu x64 server with the latest galaxy_central of Oct 4th... An export of the history sized 2.5Gb was ok. However large exports (like 10Gb) make the server instantly crash (within a few seconds) without anything significant in the galaxy.log. The apache server is still

[galaxy-dev] Database migration error

2012-10-11 Thread Bossers, Alex
After a fresh galaxy-dist pull today (no update for various reasons) the instance was running ok on the default sqlight database. When I migrated back the setting to use the MySQL database it complained during startup about having found an old version of the database and I need to upgrade.

Re: [galaxy-dev] Database migration error

2012-10-12 Thread Bossers, Alex
Some additional info; Actually the errors already started at migrate version 93-94. I just restored the version to prior upgrade to check any other errors. There were some create errors. I am not sure if these come from the \n\t statements in the sysntax or whether that is just an error log

[galaxy-dev] Error: updating quotas galaxy_dist

2012-11-12 Thread Bossers, Alex
Dear all, I have an today up-to-date galaxy-dist running (7986:12fcd068b12e). All seems to work fine. However in the admin panel when I make a quotum it works unless I let it make default at the same time or allocate groups of users to the quota. Just creating the quotem works fine without any

[galaxy-dev] Error: change attributes generates error on fresh dist-release

2012-11-12 Thread Bossers, Alex
Hi All, Due to previous DB errors we decided to let galaxy-dist repopulate the database (MySQL). We purged all tables from the DB and when restarting galaxy it repopulates the DB on the fly while doing all migration steps. A nicely running galaxy as the result. I encountered a strange error

Re: [galaxy-dev] Error: updating quotas galaxy_dist

2012-11-12 Thread Bossers, Alex
...@bx.psu.edu] Verzonden: maandag 12 november 2012 20:03 To: Bossers, Alex Cc: Galaxy Dev List Onderwerp: Re: [galaxy-dev] Error: updating quotas galaxy_dist On Nov 12, 2012, at 5:38 AM, Bossers, Alex wrote: Dear all, I have an today up-to-date galaxy-dist running (7986:12fcd068b12e). All seems

Re: [galaxy-dev] Errors in creating galaxy DB in MySQL for fresh galaxy-dist

2012-11-13 Thread Bossers, Alex
if it solves issues or upgrades better Alex -Oorspronkelijk bericht- Van: Hans-Rudolf Hotz [mailto:h...@fmi.ch] Verzonden: dinsdag 13 november 2012 14:16 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Errors in creating galaxy DB in MySQL for fresh galaxy

Re: [galaxy-dev] Error: updating user hist size (was error updating quotas) galaxy_dist

2012-11-13 Thread Bossers, Alex
...@bx.psu.edu] Verzonden: dinsdag 13 november 2012 16:45 Aan: Bossers, Alex CC: Galaxy Dev List Onderwerp: Re: [galaxy-dev] Error: updating quotas galaxy_dist On Nov 12, 2012, at 2:43 PM, Nate Coraor wrote: On Nov 12, 2012, at 2:35 PM, Bossers, Alex wrote: Nate, crapthat fixed

Re: [galaxy-dev] Error: updating quotas galaxy_dist

2012-11-13 Thread Bossers, Alex
-Oorspronkelijk bericht- Van: Nate Coraor [mailto:n...@bx.psu.edu] Verzonden: dinsdag 13 november 2012 16:45 Aan: Bossers, Alex CC: Galaxy Dev List Onderwerp: Re: [galaxy-dev] Error: updating quotas galaxy_dist On Nov 12, 2012, at 2:43 PM, Nate Coraor wrote: On Nov 12, 2012, at 2:35 PM, Bossers

Re: [galaxy-dev] Can't edit galaxy workflow

2012-11-15 Thread Bossers, Alex
Dannon, I wanted to apply the patch as well on our fresh instance. But it fails with the error of uncomitted changes.. But we only pull/merge/update using hg nothing else we do with itany clues? We only locally modified files of course (like the wsgi.ini files and loc files). $ hg patch

Re: [galaxy-dev] multithreaded tools

2012-11-26 Thread Bossers, Alex
Andreas, Yes this is possible. You can also have a look at the ncbi blast+ tools written by Peter. The same is true. Usually the tool wrappers (xml) have an option preconfigured how many threads can be used... You can adjust these directly in the xml OR as we did we added the option to be

Re: [galaxy-dev] multithreaded tools

2012-11-27 Thread Bossers, Alex
Andreas, I am not sure if you can call these surprises. Some tools (which I highly appreciate) of Peter have been parallelised to get the job done more quickly. I earlier mentioned the ncbi blast+ wrappers but there the tool by itself handles the multithreading. Other tools I am aware that use a

[galaxy-dev] Data/history/user export and import

2012-11-29 Thread Bossers, Alex
Dear all, Would it be possible somehow to not only export a single history of a user (to file) but also all histories of a user in one go. Or even all user-bound histories/settings and such? I would like to import them into another galaxy instance (basically from our internal development

Re: [galaxy-dev] Data/history/user export and import

2012-11-30 Thread Bossers, Alex
instance into a fresh onebut failed due to all sorts of unpredictable errors.. Alex -Oorspronkelijk bericht- Van: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Verzonden: donderdag 29 november 2012 17:35 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Galaxy-dev Onderwerp: Re

Re: [galaxy-dev] Changing interface design

2012-11-30 Thread Bossers, Alex
Philippe, As far as I know most of the styling is in galaxydir/static/june_2007_style/blue/base.css or the other stylesheets present in that location. Changes might only be visible when restarting the instance though! Alex Van: galaxy-dev-boun...@lists.bx.psu.edu

Re: [galaxy-dev] 回复: Speed up the galaxy

2012-12-04 Thread Bossers, Alex
Hi I presume the best way to optimise your current problem is to evaluate whether you really need to groom your data!? If its old data presumably yes, but if it is recent data in Illumina 1.8+ encoding(http://en.wikipedia.org/wiki/FASTQ_format) it is not necessary speedup 100% :-) Groom

Re: [galaxy-dev] 回复: 回复: Speed up the galaxy

2012-12-04 Thread Bossers, Alex
! Alex Van: 泽 蔡 [caizexi...@yahoo.com.cn] Verzonden: dinsdag 4 december 2012 16:41 To: Bossers, Alex Cc: galaxy-dev@lists.bx.psu.edu Onderwerp: 回复: [galaxy-dev] 回复: Speed up the galaxy Hi Alex I look the page of wikipedia, but I have a little confused. We sequenced

[galaxy-dev] bai file missing in history export?!

2012-12-13 Thread Bossers, Alex
Dear all, Are we the only ones that are missing bam index files (the .bai) when exporting a history that contains for instance bowtie mapped reads. In the original history we can save the bam and bai files but after export to a file (tgz) and later import into another (or the same) galaxy

Re: [galaxy-dev] bai file missing in history export?!

2012-12-17 Thread Bossers, Alex
Thanks. We'll test it shortly. These are usually small files (not the actual index). Alex -Oorspronkelijk bericht- Van: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Verzonden: vrijdag 14 december 2012 17:59 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev

Re: [galaxy-dev] Integrating generated graphics from cli tool?

2012-12-17 Thread Bossers, Alex
Samual, We do the same as Peter mentioned. We generate pdfs or you could generate a mixed datatype html file linking to seperate documents/images (like the fastQC tool). If you get the export to png working on a headless server without desktop/gui..please let me know. In our hands it only works

Re: [galaxy-dev] producing HTML output with images

2012-12-19 Thread Bossers, Alex
Have a look at the wiki there is a step-by-step example if I remember correctly. Furthermore, another tool which uses this kind of output is the fastQC tool (available in the toolshed). Make sure to have the html sanitize option OFF in your universe_wsgi.ini file. Alex

Re: [galaxy-dev] Integrating generated graphics from cli tool?

2012-12-20 Thread Bossers, Alex
Ross, Thanks! I will check it out. Alex Van: Ross [mailto:ross.laza...@gmail.com] Verzonden: donderdag 20 december 2012 9:52 Aan: Bossers, Alex CC: Samuel Lampa; galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Integrating generated graphics from cli tool? Alex, xvfb http://www.xfree86

[galaxy-dev] Toolshed tools minimal requirments for submission

2013-02-04 Thread Bossers, Alex
Hi All, We are experimenting with local toolsheds for tool maintainability. On the old galaxy wiki I can remember there was a short tutorial or small description of the minimal requirements of a tool to be submitted to the toolshed. Actually we submitted some. However we seem unable to

Re: [galaxy-dev] Toolshed tools minimal requirments for submission

2013-02-04 Thread Bossers, Alex
Alex Van: Greg Von Kuster [mailto:g...@bx.psu.edu] Verzonden: maandag 4 februari 2013 16:25 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] Toolshed tools minimal requirments for submission Hello Alex, In very general terms, a repository should include everything

Re: [galaxy-dev] Bug in Galaxy Reports tool

2013-02-14 Thread Bossers, Alex
Hhhmm seems to behave normally in our running (latest) dist release 8530:a4113cc1cb5e tip Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Greg Von Kuster Verzonden: dinsdag 12 februari 2013 12:29 Aan:

Re: [galaxy-dev] Bug in Galaxy Reports tool

2013-02-14 Thread Bossers, Alex
Hhhmmm.. and now it doesn't and reproduces what Joachim reported... -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: donderdag 14 februari 2013 11:45 Aan: Greg Von Kuster; joachim.ja...@vib.be

Re: [galaxy-dev] Knowing who is currently logged into your system

2013-03-28 Thread Bossers, Alex
Akshay If you have galaxy_reports running on your server you can see the most likely logged in users under: Users/Date of last login when you query it for 0 days. You at least have a login per day (not on the hour though). For restarting purposes we ignore viewers and monitor the running jobs in

Re: [galaxy-dev] Knowing who is currently logged into your system

2013-03-29 Thread Bossers, Alex
] Verzonden: donderdag 28 maart 2013 15:22 Aan: Bossers, Alex CC: Jennifer Jackson; Galaxy Dev Onderwerp: Re: [galaxy-dev] Knowing who is currently logged into your system Hey Alex, Thanks for the quick response. The reason why I asked this question is because we reimplemented our plugin WS

Re: [galaxy-dev] Track Job Runtime

2013-05-08 Thread Bossers, Alex
+1 for me! Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [galaxy-dev-boun...@lists.bx.psu.edu] namens Peter Cock [p.j.a.c...@googlemail.com] Verzonden: woensdag 8 mei 2013 12:06 To: Geert Vandeweyer Cc: galaxy-dev@lists.bx.psu.edu Onderwerp: Re:

Re: [galaxy-dev] Storage question for Galaxy-Admins

2013-05-30 Thread Bossers, Alex
Raj, maybe others have a different view on this but I think just throwing you a number is quite useless. It all depends on YOUR data storage strategy/policy. How long can researchers store/use their data. What are their maxed quota...Is it backuped elsewhere, how many users. Is it public

Re: [galaxy-dev] import Workflow from public Galaxy to local instance

2013-05-30 Thread Bossers, Alex
Andreas, export your history to tgz. then locally import it. I have to say that we do this for backup purposesbut it is a pain.exporting takes sometimes ages even for small histories. I am not sure how well synced your databases and such should be.(unique identifiers and

Re: [galaxy-dev] account avatar

2013-06-24 Thread Bossers, Alex
If I remember you have to associate a gravatar to your registered email. http://en.wikipedia.org/wiki/Gravatar Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Philipe Moncuquet Verzonden: maandag 24 juni 2013 7:42 Aan:

Re: [galaxy-dev] allow users for specifying the number of CPUs

2013-07-10 Thread Bossers, Alex
Jens, The obvious way to temporarily solve this is by adding an additional select in your tool xml having a low default core setting where users can select more cores...this is however not user specific unless you let another wrapper deal with that. This solution we use for the blast wrappers

Re: [galaxy-dev] Configuring the time of permanently deleting data sets.

2013-07-10 Thread Bossers, Alex
Ricardo, You can configure galaxy such that it will allow users to permanently delete and purge datasets from their own histories. After deleting by pressing the cross...select 'include deleted datasets' from the history menu. There you can undelete but also purge immediately from disk. So

Re: [galaxy-dev] tool not runing in workflow

2013-08-27 Thread Bossers, Alex
Thomas, Did you generate the work flow from scratch or did you make a simple analysis in the history and extracted a work flow from that? The latter we usually do without problems whatever...but we don't use the mothur tools though... Alex Van: galaxy-dev-boun...@lists.bx.psu.edu

Re: [galaxy-dev] Pick-you-own columns in BLAST+ tabular output

2014-01-17 Thread Bossers, Alex
Peter, We will definitely give them a try. I never understood why the tabular outputs did have an option to include the defline/hit decription. Just for that we needed to use the cloggy XML output and parse that into a table again. Conserved header names are more useful to us than having column

[galaxy-dev] Indexes separator in tool

2014-02-03 Thread Bossers, Alex
Not sure if this question or solution has passed this list already but couldn't find anything in the archive. Is it possible to somehow insert separator lines between groups of for instance bowtie2 indexes? One of our tool displays it like below (the - lines); I would like to add

Re: [galaxy-dev] running tools within tool

2014-02-05 Thread Bossers, Alex
Ketan, Are workflows not the way to go for this? We have similar tools that are usually run in sequence. We made them all separate to allow reusing them elsewhere. For these linked tools one could write a superscript/wrapper or design a workflow which can be public or privately shared. Best

Re: [galaxy-dev] Strange issue with datatypes in Galaxy version of last week

2014-03-25 Thread Bossers, Alex
Pieter, I just experienced the same with another generic tabular .tab file output. It broke the filename at dash without any extension. The file itself was ok, just the name. Alex Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens Lukasse, Pieter

Re: [galaxy-dev] Citing Galaxy + Toolshed in an app note of a small tool

2014-03-28 Thread Bossers, Alex
James, I have been looking for it as well some while ago. Would be good to post it somewhere on the wiki in a prominent place...how to cite... Thx Alex -Oorspronkelijk bericht- Van: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] Namens James Taylor