Re: [galaxy-dev] galaxy-dev Digest, Vol 101, Issue 29

2014-11-20 Thread Dooley, Damion
Well, here's one config that should work. I'll guess that you have the same cleanup_datasets/ folder contents as I do so... having logged in as user that galaxy runs under, doing a crontab -e on command line should get you crontab settings for that user. I have an older longer line that

Re: [galaxy-dev] master_api_key currently doesn't benefit from a real admin's key?!

2014-11-21 Thread Dooley, Damion
Ok, I'll figure out what I can take on here in terms of being more systematic about determining the various error cases/fixes visa vis the master_api_key and the API, and will get back to you. Having the master key work without a user object does sound like the pure way to go. Thanks, d.

[galaxy-dev] No API way to delete a galaxy data library folder?

2014-12-04 Thread Dooley, Damion
I just wanted to verify that this is the case? I've put in a Trello card requesting this feature for the API. My app creates and manages the content of some data library folders for the versioned data project. Regards, Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory,

Re: [galaxy-dev] disk space does not add up...

2014-12-17 Thread Dooley, Damion
Just a small question about this - you have purge_datasets.sh, and then delete_datasets.sh . Shouldn't it be the other way around, since purging only works on the deleted datasets? (I realise this doesn't address your main issue, since running it twice should have maximized free space.)

[galaxy-dev] Tool param type library_data

2015-01-14 Thread Dooley, Damion
I just discovered a scant reference to this on the ToolSyntax page, and tracked it down to something that looks like it was introduced around 2011: a LibraryDatasetToolParameter http://bitbucket.org/galaxy/galaxy-central/changeset/8553b02ce9ee/ changeset: 8553b02ce9ee user:kanwei

Re: [galaxy-dev] Tool param type library_data

2015-01-19 Thread Dooley, Damion
Just to summarize what I found about getting tool parameter param type=library_data going again (though a future expansion of dataset parameters to handle this would be great, esp. if one can specify a particular data library): 1) Aysam's patch (thanks!) 2) Tool_form.mako has a hardcoded url

Re: [galaxy-dev] Tool param type library_data (Dooley, Damion)

2015-01-20 Thread Dooley, Damion
I was successful getting library dataset selection and form submission to happen within tool form tool form input param type=library_data ... - Yay! But it appears one last fix (besides the url: /visualization/list_libraries,' bug) is needed to enable history tool item to be RERUN. So if a

Re: [galaxy-dev] Tool param type library_data

2015-01-15 Thread Dooley, Damion
, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada From: James Taylor [ja...@jamestaylor.org] Sent: Thursday, January 15, 2015 12:53 AM To: Dooley, Damion Cc

[galaxy-dev] Tool test failure - I could use some help...

2015-02-11 Thread Dooley, Damion
I was trying to track down why an attempt to test my tool is eventually failing with: ValueError: No such test TestForTool_ffp_phylogeny In my case the tool code is located in a Galaxy's tool shed folder, so I'm guessing that might have something to do with it? Has someone come up with a

Re: [galaxy-dev] Tool test failure - I could use some help...

2015-02-12 Thread Dooley, Damion
From: Peter Cock [p.j.a.c...@googlemail.com] Sent: Thursday, February 12, 2015 3:39 AM To: Dooley, Damion Cc: galaxy-...@lists.bx.psu.edu Subject: Re: [galaxy-dev] Tool test failure - I could use some help... On Thu, Feb 12, 2015 at 2:41 AM, Dooley, Damion

Re: [galaxy-dev] No API way to delete a galaxy data library folder?

2015-01-12 Thread Dooley, Damion
Hi Martin - Following up on this - I think your API folder delete commit is : https://bitbucket.org/galaxy/galaxy-central/commits/8f76a6abc5d7d5c98b6c148c4cfe75cc1c159e90 ? I was wondering how to find out more about this API call. Not knowing the guts of the Galaxy API code much, is it a

Re: [galaxy-dev] Galaxy Bioblend option for importing dataset into a library? (Nicola Soranzo)

2015-01-12 Thread Dooley, Damion
Hi Damion, I finally got to implement this, see method copy_from_dataset() in this commit: https://github.com/afgane/bioblend/commit/bc6b7cb71abb25aa109b85b1ff24e73aadac5ce4 Thanks Nicola! Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control

Re: [galaxy-dev] Tool test failure

2015-02-13 Thread Dooley, Damion
I tried using the default config/job_conf.xml but that didn't make a difference. I'll just try testing on a different solo galaxy instance, and will report back. I'm guessing it will work elsewhere. Message: 3 ... Subject: Re: [galaxy-dev] Tool test failure - I could use some help... ...

Re: [galaxy-dev] Comment on Training Documentation

2015-03-15 Thread Dooley, Damion
Darn, last week I wrote I'll let trainees know that incrementing a tool version number leads to a separately selectable tool version to run. To keep an up-to-date Galaxy install is to engage the admin to be bringing in these tool versions/choices more frequently even though they functionally

Re: [galaxy-dev] Comment on Training Documentation

2015-03-13 Thread Dooley, Damion
[jmchil...@gmail.com] Sent: Friday, March 13, 2015 7:56 AM To: Peter Cock Cc: Martin Čech; galaxy-...@lists.bx.psu.edu; Hsiao, William; Dooley, Damion Subject: Re: [galaxy-dev] Comment on Training Documentation Awesome work Damion - thanks for publishing and sharing these! I hope the workshop goes well

[galaxy-dev] Comment on Training Documentation

2015-03-12 Thread Dooley, Damion
I've prepared a few slide-decks for an in-house Galaxy tool-development workshop, available at https://github.com/Public-Health-Bioinformatics/galaxy-tool-tutorials in pdf and libre office odp format. I thought others might appreciate them or have feedback. I see now the

Re: [galaxy-dev] Tool param type library_data (Dooley, Damion)

2015-03-02 Thread Dooley, Damion
I understand a new tool form module is rolling out in the next few weeks. Will anything change in the HTML form hidden input submit fields? Right now tool forms have the equivalent of: form id=tool_form name=tool_form action=../../../tool_runner target=galaxy_main method=post

Re: [galaxy-dev] Tool Testing: field inputs that occur inside repeat tag - semi resolved.

2015-02-27 Thread Dooley, Damion
First, hey Peter, thanks for input! I'd seen the explicit piping before, couldn't remember its format though; I will switch to it. Well, after a morning of testing, I see the test system is actually finding the repeat section variables. It looks like its error Parameter filter_column

Re: [galaxy-dev] Tool Testing: field inputs that occur inside repeat tag - resolved

2015-02-27 Thread Dooley, Damion
, British Columbia, V5Z 4R4 Canada From: Peter Cock [p.j.a.c...@googlemail.com] Sent: Friday, February 27, 2015 1:39 PM To: Dooley, Damion Cc: galaxy-...@lists.bx.psu.edu Subject: Re: Tool Testing: field inputs that occur inside repeat tag - semi resolved

[galaxy-dev] Subject: Serving Galaxy at a sub directory - symptoms without filter-with = proxy-prefix

2015-02-25 Thread Dooley, Damion
This info is definitely useful! I ran into this exact same problem last week, trying to set up a new instance of galaxy from the mercurial repo. I was re-using a previous install's apache config; saw the same web page results. Had to go to the galaxy web docs to track down that filter-with

[galaxy-dev] FW: Tool Testing: field inputs that occur inside repeat tag

2015-02-26 Thread Dooley, Damion
Slightly garbled there ... meant to say Help appreciated once again, Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada

[galaxy-dev] Tool Testing: field inputs that occur inside repeat tag

2015-02-26 Thread Dooley, Damion
Helop aI've been testing (using planemo) some tools scheduled for toolshed publication. My first test works, but Galaxy reports that the second one fails with: Parameter %s requires a value, but has no legal values defined % self.name AssertionError: Parameter filter_column requires a value,

Re: [galaxy-dev] find UUID of current history in tool XML wrapper?

2015-05-05 Thread Dooley, Damion
About 1. find UUID of current history in tool XML wrapper? (Ben Bimber) 2. Re: find UUID of current history in tool XML wrapper? (John Chilton) I think this will work for you, I've simplified the code. I was able to do this somewhat circuitously (=bonfire of time) for my upcoming

Re: [galaxy-dev] find UUID of current history in tool XML wrapper?

2015-05-05 Thread Dooley, Damion
P.s. I tried using BioBlend and(or) the Galaxy API to get a given user's current history but found there was no way to do so. Seems like there is occasionally a tension between plaform by design (reduced instruction set, occasionally with security in mind, or dev resource limitations) and

Re: [galaxy-dev] find UUID of current history in tool XML wrapper?

2015-05-05 Thread Dooley, Damion
First, John, that $output_dataset.creating_job.history.id looks great! Ok, Dannon, I see various merits of stateless design - always providing server processes with the entire input array (files, params) in which no server state memory is referenced for a given user/agent task (aside from user

Re: [galaxy-dev] Older galaxy I'm keeping alive by drip feed, has problem restarting when I turn debug off.

2015-04-15 Thread Dooley, Damion
Ok, Daniel I don't really know egg vs site-packages install or how to change that; I tried upgrading our python 2.6 Paste to 1.7.5 but that didn't effect a change. Dannon I tried toasting compiled_templates directory, to no avail. The site was last upgraded in 2012. I'm afraid to mess with

Re: [galaxy-dev] Cosmetic Makeblastdb error promulgated through wrapper

2015-07-04 Thread Dooley, Damion
Avenue, Vancouver, British Columbia, V5Z 4R4 Canada From: Peter Cock [p.j.a.c...@googlemail.com] Sent: Saturday, July 04, 2015 8:11 AM To: Dooley, Damion Cc: galaxy-...@lists.bx.psu.edu Subject: Re: [galaxy-dev] Cosmetic Makeblastdb error promulgated through

Re: [galaxy-dev] Cosmetic Makeblastdb error promulgated through wrapper

2015-07-04 Thread Dooley, Damion
Cock [p.j.a.c...@googlemail.com] Sent: Saturday, July 04, 2015 9:27 AM To: Dooley, Damion Cc: galaxy-...@lists.bx.psu.edu Subject: Re: [galaxy-dev] Cosmetic Makeblastdb error promulgated through wrapper ... What is the error code? It might still be zero (which is fine for a warning only). I've

[galaxy-dev] Cosmetic Makeblastdb error promulgated through wrapper

2015-07-04 Thread Dooley, Damion
Makeblastdb can spit out warning notices when a higher count of N ambiguous nucleotides occurs in the first row of fasta data, but goes ahead and completes the blast database. Error: (1431.1) FASTA-Reader: Warning: FASTA-Reader: First data line in seq is about 45% ambiguous nucleotides

[galaxy-dev] Trying to install GATK on up-to-date Galaxy install

2015-11-04 Thread Dooley, Damion
I seem to run into a bottleneck with the .’package_pixman_0_32_4’. This seems to happen with both boris and devteam versions? The same error is preventing cairo from installing.

Re: [galaxy-dev] Cosmetic Makeblastdb error promulgated through wrapper

2015-07-07 Thread Dooley, Damion
So it does return error code 0, thankfully. I've dropped the workaround on https://github.com/peterjc/galaxy_blast/issues/40 , and could do the pull request process in a few weeks. d. ... What is the error code? It might still be zero (which is fine for a warning only). I've reopened

Re: [galaxy-dev] Tool code for symlinking a data collection from input to output?

2015-11-17 Thread Dooley, Damion
Ah, I can see how symlinking could lead to file management issues. Well, we were trying to avoid the situation where use of our qc tool would require customizing any subsequent tools in a workflow, and as well, reduce disk overhead of hundred megabyte files being passed along in a workflow. So

[galaxy-dev] Picard sam2fastq tool can output file including both single and paired reads?

2015-09-16 Thread Dooley, Damion
A researcher here was trying to use Galaxy Picard sam2fastq tool to generate a single fastq file from a sam file that has a mix of paired and unpaired data. She was thinking the second input on the sheet might control this: > Do you want to output a fastq file per read group (two fastq files

Re: [galaxy-dev] galaxy.ini tool_dependency_dir change

2015-09-09 Thread Dooley, Damion
ntrol 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada From: Will Holtz [who...@lygos.com] Sent: Wednesday, September 09, 2015 11:10 AM To: Dooley, Damion Cc: galaxy-...@lists.bx.psu.edu Subject: Re: [galaxy-dev] galaxy.ini tool_dependency_dir c

[galaxy-dev] galaxy.ini tool_dependency_dir change

2015-09-09 Thread Dooley, Damion
On a VM I moved the tool_dependency_dir folder to another mount since it was getting so large that the smallish main mount was full (and changed galaxy.ini, restarted galaxy, and checked that permissions were appropriate for galaxy user). But I'm finding I have to reinstall various tool

[galaxy-dev] _JAVA_OPTIONS config parameter in job_conf.xml.sample_advanced

2015-09-24 Thread Dooley, Damion
Wondering if anyone has reported this for the doc/sample file team: Isn't the java config example line in that file wrong (at least for my java 1.6): -Xmx=6GB With a setting of -Xmx=10g, Picard wouldn't run sortSam, instead this stderr text: * Fatal error: Exit code 1 ()

Re: [galaxy-dev] Publish tool with Python dependencies to the toolshed

2015-12-03 Thread Dooley, Damion
Related to this thread, my report calc tool needs a few python packages, but I think they are generic enough to be in python 2.6, 2.7 or 3.x , so can I specify the packages without specifying the python version? (I'm looking at the

Re: [galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control

2016-01-11 Thread Dooley, Damion
t trying to provide the all-out iPython approach. D. On 2016-01-11, 12:03 PM, "Bob Harris" <rshar...@bx.psu.edu> wrote: >On Jan 11, 2016, at 2:42 PM, Dooley, Damion wrote: >> ... we're testing out a basic scripting language ... meant to provide >>[folks] with >&g

[galaxy-dev] Any way to prime the value of a tool text field parameter dynamically?

2016-06-08 Thread Dooley, Damion
I have a need to have the default value of a text parameter : Set dynamically, as powered by say a call to a function in , much like a dynamic_options="get_rule_section(recipe_file)" call. Has anyone done that somehow without hacking Galaxy code? A user can then edit the text. The default

Re: [galaxy-dev] how to get raw input from GUI

2016-06-14 Thread Dooley, Damion
A general note, besides which sounds like a fine choice, a technique I've used where the form's input might have some wonky characters in it, including carriage returns, but these need to be received and processed via a command line, is to use encode(): $rules.encode('base64').replace('\n','')

[galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control

2016-01-11 Thread Dooley, Damion
Folks, we're testing out a basic scripting language and interpreter for report writing and quality control that is meant to provide both command-line programmers and Galaxy platform researchers and admins with ways to tweak workflow quality control behaviour without having to be programmers

Re: [galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control

2016-02-09 Thread Dooley, Damion
Hi folks, I'm back with one more feeler to gauge interest in the approach we are trying out for a Galaxy quality control tool to interject into existing bioinformatics pipelines. With some nudging (thanks Bob) I've implemented basic infix math expressions. As well we're trying out the inclusion

[galaxy-dev] access system variables in tool xml (Matthias De Smet)

2016-01-27 Thread Dooley, Damion
Others might have responded to this, and I can't remember the very latest approach, but I used the approach below... Its not easy though since api is read via script [BTW, topically, I still need on a regular basis!], but is passed over to command line app securely via a . For error situation

Re: [galaxy-dev] Scaling tools: data available? (Peter van Heusden)

2016-03-19 Thread Dooley, Damion
If you are looking for a simple python program to log cpu% and memory of another executable, then analyze.py might do. Its in https://github.com/Public-Health-Bioinformatics/kipper/tree/master/RDP-test -case along with a few scripts that show examples of its use. Damion >> >> On 02/21/2016 11:13

[galaxy-dev] Error after loading up bebatut MetaPhlAn2 to our local Galaxy instance

2016-11-22 Thread Dooley, Damion
After loading up MetaPhlAn2 (8991e05c44e4) from toolshed and attaching db_v20, I tried running a few fasta files on it, including the tool's test-data/input_sequences.fasta file, but after about a minute of churning I keep getting this error: Fatal error: Exit code 1 () … Traceback (most recent