[galaxy-dev] Error after loading up bebatut MetaPhlAn2 to our local Galaxy instance
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 call last): File "/usr/local/galaxy/shared/tool_dependency/metaphlan2/2.5.0/bebatut/package_ metaphlan2_2_5_0/43a80f92815f/metaphlan2.py", line 1172, in tree = TaxTree( mpa_pkl, ignore_markers ) File "/usr/local/galaxy/shared/tool_dependency/metaphlan2/2.5.0/bebatut/package_ metaphlan2_2_5_0/43a80f92815f/metaphlan2.py", line 857, in __init__ clades_txt = ((l.strip().split("|"),n) for l,n in mpa_pkl['taxonomy'].items()) AttributeError: 'list' object has no attribute 'items' I believe the database is connected properly, but would the tool run for a while even if it wasn't? It seems like the mpa_pkl file data is loaded via the --mpa_pkl attribute as in tool command line: which bowtie2 || exit 200) && metaphlan2.py /galaxy_data/production1/files/013/dataset_13546.dat -o /galaxy_data/production1/files/013/dataset_13547.dat --input_type fasta --bowtie2_exe `which bowtie2` --bowtie2db /usr/local/packages/metaphlan2/db_v20/mpa_v20_m200 --mpa_pkl /usr/local/packages/metaphlan2/db_v20/mpa_v20_m200".pkl" --no_map -t rel_ab --tax_lev a --min_cu_len 2000 --min_alignment_len 0 --stat_q 0.1 -s /galaxy_data/production1/files/013/dataset_13548.dat Tool's xml file does a touch of funny business with the mpa_v20_m200".pkl" file name parameter, but I guess that works if no one else has a problem with it. Thx for any info, Damion ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Any way to prime the value of a tool text field parameter dynamically?
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 depends on a previous selection (e.g. recipe_file input). Thanks, Damion ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Scaling tools: data available? (Peter van Heusden)
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 PM, Peter van Heusden wrote: >> >> Hi there >> >> We're researching the resource (CPU time and memory) requirements for >>RNA >> STAR at the moment. Specifically, we'd like to build up a database of >>input >> size to resource usage so that we can use this to feed a dynamic >> destination mapper (currently our STAR configuration uses a thumbsuck >>for >> RAM and CPU requirements that is not optimal but works in many cases). >> >> Has anyone collected these metrics before? And more generally, is anyone >> collecting metrics for a range of bioinformatics tools? A database like >> this could be very useful! >> >> Thanks! >> 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control
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 of ontology metadata within report data to encourage data import/export/comparison. The goal is to make it easy to see and change quality control metrics (without having to recompile code or modify Galaxy workflow mechanics.) The QC scripting language/interpreter as a Galaxy tool lets us read in text file(s) - some assembly contig data say - and then run a program (a set of rules) like: store( 200 report/contigs/contig_count_QC_threshold ) store( 20 report/contigs/contig_N50_QC_threshold ) store( 2000 report/contigs/contig_N99_QC_threshold ) if( ( genome_size_ratio > genome_size_ratio_QC_threshold ) fail(qc "Failed genome size ratio threshold") ) store( statisticN( contig_lengths 50 ) report/contigs/contig_N50 ) store( statisticN( contig_lengths 99 ) report/contigs/contig_N99 ) if( contig_N50 < contig_N50_QC_threshold fail(qc "Failed minimum N50 contig length threshold") ) if( contig_N99 < contig_N99_QC_threshold fail(qc "Failed minimum N99 contig length threshold") ) if( report/contigs/contigs_count > contig_count_QC_threshold fail(job "Failed minimum contig count threshold" ) ) Which is like a generic, basic function(parameter1 parameter2...) type of language. On a good run this yields a JSON report like: { "title": "RCQC Quality Control Report", "tool_version": "0.0.7", "job": { "status": "ok" }, "quality_control": { "status": "ok" }, "date": "2016-02-09 09:21", "contigs": { "contig_lengths": [ 128, 172, 221, 224, 238, 230, 240, 246, 407, ... , 242, 2284, 1506], "genome_size_ratio_QC_threshold": 0.10001, "contig_N99_QC_threshold": 2000, "assembly_genome_size": 4615592, "genome_size_ratio": 0.04970310891496809, "contig_N50": 427122, "contig_N99": 8542, "contig_count_QC_threshold": 200, "contig_count": 44, "reference_genome_identifier": "serovar Typhimurium LT2", "reference_genome_size": 4857000, "contig_N50_QC_threshold": 20 }, "@context": { "contigs": "http://purl.obolibrary.org/obo/SO_0001462;, "genome_size_ratio_QC_threshold": "http://purl.obolibrary.org/obo/GenEpiO_0001564;, "contig_N99_QC_threshold": "http://purl.obolibrary.org/obo/GenEpiO_0001566;, "assembly_genome_size": "http://purl.obolibrary.org/obo/GenEpiO_0001561;, "genome_size_ratio": "http://purl.obolibrary.org/obo/GenEpiO_0001563;, "contig_N50": "http://purl.obolibrary.org/obo/OBI_0001941;, "contig_N99": "http://purl.obolibrary.org/obo/GenEpiO_0001570;, "contig_count_QC_threshold": "http://purl.obolibrary.org/obo/GenEpiO_0001571;, "contig_count": "http://purl.obolibrary.org/obo/GenEpiO_093;, "reference_genome_identifier": "http://purl.obolibrary.org/obo/GenEpiO_0001562;, "date": "http://purl.obolibrary.org/obo/IAO_416;, "reference_genome_size": "http://purl.obolibrary.org/obo/GenEpiO_0001560;, "contig_N50_QC_threshold": "http://purl.obolibrary.org/obo/GenEpiO_0001565; } } So we'd appreciate any advice on roadblocks or desired features you perceive on this... - Damion > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] access system variables in tool xml (Matthias De Smet)
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 messaging back to user I was using a dynamic box radio drill_down input. All this code is in toolshed under "versioned_data". Teasing out what you need might require some work though - the code also has a chunk of stuff for maintaining use of an administrator's api key as well as the user's since the app needed to do admin level api work on behalf of a user. >-- > >Message: 11 >Date: Wed, 27 Jan 2016 12:42:17 + >From: Matthias De Smet>... >Hi again > >I’m trying to create a tool that interacts with galaxy through the API. >For this, I need to get the users API key (or equivalent) en the domain >name of the Galaxy host. > >The purpose of this tool is to get data and put it in a data library, so >I suppose I need to use the API. Or is there another way to do this with >a tool? > >Thanks! >Matthias #assert $__user__, Exception( 'You must be logged in to use this tool.' ) versioned_data.py ... -O "$__app__.security.encode_id($log.id)" --api_info_path "$api_info_path" ##Actually a file path to configfile that holds api key ... ${__user__.api_keys[0].key} $api_info And over in versioned_data_form.py ( there's a reference to "set_trans()" which feeds through to set_user_api() below... import vdb_retrieval def vdb_init_tool_user(trans): """ Retrieves a user's api key if they have one, otherwise lets them know they need one This function is automatically called from versioned_data.xml form on presentation to user Note that this is how self.api_url gets back into form, for passage back to 2nd call via versioned_data.py self.api_key is passed via secure construct. ALSO: squeezing history_id in this way since no other way to pass it. "trans" is provided only by tool form presentation via BUT NOW SEE John Chilton's: https://gist.github.com/jmchilton/27c5bb05e155a611294d See galaxy source code at https://galaxy-dist.readthedocs.org/en/latest/_modules/galaxy/web/framework .html, See http://dev.list.galaxyproject.org/error-using-get-user-id-in-xml-file-in-ne w-Galaxy-td4665274.html See http://dev.list.galaxyproject.org/hg-galaxy-2780-Real-Job-tm-support-for-th e-library-upload-to-td4133384.html master api key, set in galaxy config: #self.master_api_key = trans.app.config.master_api_key """ global retrieval_obj api_url = trans.request.application_url + '/api' history_id = str(trans.security.encode_id(trans.history.id)) user_api_key = None if trans.user: user_name = trans.user.username if trans.user.api_keys and len(trans.user.api_keys) > 0: user_api_key = trans.user.api_keys[0].key #First key is always the active one? items = [ { 'name': user_name, 'value': api_url + '-' + history_id, 'options':[], 'selected': True } ] else: items = [ { 'name': user_name + ' - Note: you need a key (see "User" menu)!', 'value': '0', 'options':[], 'selected': False } ] else: items = [ { 'name': 'You need to be logged in to use this tool!', 'value': '1', 'options':[], 'selected': False } ] retrieval_obj = vdb_retrieval.VDBRetrieval() retrieval_obj.set_trans(api_url, history_id, user_api_key) return items And over in tool xml's target code (versioned_data.py) it includes vdb_retrieval.py BUT THIS HAS A LOT OF STUFF YOU PROBABLY DON'T NEED! Sorry!: from bioblend.galaxy import GalaxyInstance class VDBRetrieval(object): def __init__(self, api_key=None, api_url=None): """ This gets either trans.x.y from call in versioned_data.xml, or it gets a call with api_key and api_url from versioned_data.py @param api_key_path string File path to temporary file containing user's galaxy api_key @param api_url string contains http://[ip]:[port] for handling galaxy api calls. """ # Initialized constants during the life of a request: self.global_retrieval_date = None self.library_id = None self.history_id = None self.data_stores = [] # Entire json library structure. item.url, type=file|folder, id, name (library path) # Note: changes to library during a request aren't reflected here. self.library = None
Re: [galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control
Hi, Thanks for quick reply, and good point about keeping math expressions familiar to most users. In this first round I settled for a simple prefix "function(parameter1 parameter2 ...)". All the python infix operators like "a + b" have equivalent prefix functions "add(a b)" so the latter are used. Yes, infix "a + b" parsing would be easier to read, and I was thinking we could try that on our next iteration (and remain backward compatible) but more opinion may shift that up! (Some other issues to tackle too: decisions about whether "/" should map to "div(a b)" or "truediv(a b)", and how to avoid conflict with our namespace method of referring to variables via a/b/c paths). I'm definitely avoiding eval() since we do have to control exactly which functions, conditionals, and loop constructs are executed. Not 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 >> ways to [do something] without having to be programmers ... >> >> if( lt(/N50 20) set(report/job/status FAIL)) >> >> Math is accomplished by python built-in math functions ... > > >It could well be that's the only way to accomplish what you want in >whatever environment you're in. But the use of prefix notation and a >funny name, for an operator like "<" that non-programmers use familiarly >as infix, would seem contrary to the stated goal that the user needn't be >a programmer. > >If math can be accomplished via python, why not "<"? By "math" do you >only mean function calls, and not arithmetic operators? Is it that >python eval() can't be used because of security issues? > >Bob H > ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] A Report Calc tool which provides a scripting language and interpreter for text mining and quality control
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 themselves. I wanted to sound-out the community about whether or not there are any basic objections to our approach, described briefly below? Currently the interpreter provides all the built-in Python operator and math functions (as well as some particular named group regular expression functions for text mining) so that users can examine given input log or data datasets for fields that need to be reported or compared with QC metric rules. The Report Calc tool takes in a file of statements (each being a function(parameter1 parameter2 ...) syntax) that look like this: set(4857000 report/contigs/reference_genome_size) set("serovar Typhimurium LT2" report/contigs/reference_genome) set(0.1 report/contigs/good_genome_size_ratio) set( statisticN(report/contigs/contig_lengths 50) report/contigs/N50) if( lt(/N50 20) set(report/job/status FAIL)) Math is accomplished by python built-in math functions (I.e. Ignore the "/" - that's a namespace syntax character). set( truediv( abs( sub( /sampleGenomeSize /referenceGenomeSize)) /referenceGenomeSize) report/contigs/sample_genome_size_ratio ) And writes any output as desired to a standard tool output folder: writeFile( pageHtml( getHtml(report) "My Report Widget") report.html ) It allows users to build a ruleset (file containing statements like the above), and process text, json, tabular datasets in their history, and it can manipulate variables, arrays and dictionaries in the tools in-memory temporary data structure namespace. It doesn't touch Galaxy's inner workings or interact with a workflow except by way of app exit codes. One can even write little text-mining programs in it: iterate( readFileByName(contigs-all.fasta) if( eq( getitem(iterator/0/value 0) ">") append( regexp(iterator/0/value "length_(?P\\d+)_") report/contigs/contig_lengths ) ) ) I'll release it shortly for review/play, with lots of documentation that describes in detail what it can/can't do, and an argument for why one might want to bother using/learning it. There are one or two irrelevant python built-in functions we might filter out (e.g. isCallable() ); so far we haven't spotted any security issues, and we've limited the flow control to only accomplish loops by iterables so there's no evident way to create infinite loops. One only iterates through files or in-memory arrays. As well suggested functionality for the wish-list now accepted! Regards, Damion ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Publish tool with Python dependencies to the toolshed
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 https://github.com/galaxyproject/tools-iuc/blob/master/packages/package_pyt hon_2_7_bcbiogff_0_6_2/tool_dependencies.xml file). Or do I need to be doing something like: pip install ... ? I'm able to upload this to our local toolshed, and it seems to install ok from there, but I see in test server galaxy log "galaxy.tools.deps WARNING 2015-12-03 22:23:02,513 Failed to resolve dependency on 'report_calc', ignoring", though tool still runs (probably because the python packages were already installed manually previously.) Much obliged, Damion Tool definition file has: report_calc tool_dependencies.xml : https://pypi.python.org/packages/source/d/dateutils/dateutils -0.6.6.tar.gz#md5=2ba7fcac03635f1f1cad0d94d785001b https://pypi.python.org/packages/source/p/pyparsing/pyparsing -2.0.6.tar.gz#md5=a2d85979e33a6600148c6383d3d8de67 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool code for symlinking a data collection from input to output?
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 wow on the second paragraph - enabling dependencies outside of tool file I/o. I agree with Eric, this will be great. Now in our current canned workflows we actually don't need this to be edited via the interface - so are there details on how to edit a workflow file directly to get this dependency of tool B on tool A in place? Thanks, Damion On 2015-11-17, 11:18 AM, "John Chilton"wrote: >Slowly trying to catch up on e-mail after a lot of travel in November >and I answered a variant of this to Damion directly, the most relevant >snippet was: > >" >I would not symbolic link the >files though. I would just take the original collection and pipe it >into the next tool and add a dummy input to the next tool >("passing_qc_text_file") that would cause the workflow to fail if the >qc fails. This is a bit hacky, but symbolic linking will break >Galaxy's deletion, purging, etc You can delete the original >dataset collection and the result would affect the files on disk for >the output collection without Galaxy having anyway to know. > >The workflow subsystem has the ability to define a connection like >this (just wait for one tool to pass before calling the next without a >input/output relationship) but it hasn't been exposed in the workflow >editor yet." > >-John ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] _JAVA_OPTIONS config parameter in job_conf.xml.sample_advanced
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 () Picked up _JAVA_OPTIONS: -Xmx=10g Invalid maximum heap size: -Xmx=10g Could not create the Java virtual machine. * I changed the tag to take out "=" so it reads: -Xmx6G and now its working fine! Had to lookup -Xmx param format on the net from: http://javahowto.blogspot.ca/2006/06/6-common-errors-in-setting-java-heap.html Regards, Damion. Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] galaxy.ini tool_dependency_dir change
Thanks for suggestion. I was hoping to have my tool dependencies folder sit alongside some other folders on a /data/ mount though. Now after some searching related to your mount idea, I'm seeing "mount --bind" as a possible solution ... anyone use this approach? Something like: mv /home/galaxy/tool_dependencies /data/irida/data/tool_dependencies mkdir /home/galaxy/tool_dependencies mount -o bind /data/irida/data/tool_dependencies /home/galaxy/tool_dependencies Regards, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 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 change Can you move the folder to a new drive, but mount that new drive at the same place within the filesystem? -Will ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] galaxy.ini tool_dependency_dir change
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 dependencies (prokka etc) to enable galaxy to find the command line executables. Is there a trick to getting the tool dependencies working again after moving the folder wholesale? Thanks, Damion Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Cosmetic Makeblastdb error promulgated through wrapper
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 https://github.com/peterjc/galaxy_blast/issues/40 for any potential Galaxy wrapper work around, 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Cosmetic Makeblastdb error promulgated through wrapper
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 (shouldn't be over 40%) At moment the NCBI Blast+ wrappers (toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_makeblastdb/0.1.01) are saying yup those are errors, but i think they should be downgraded to just Notices? If the tool is part of a workflow it fails - on db's like RDP RNA this is quite a nuisance. Anyone else run into the same thing? d. Also see: http://www.acgt.me/blog/2014/5/15/fun-with-an-error-message-from-ncbi-blast Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] find UUID of current history in tool XML wrapper?
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 Versioned Data tool. In your tool XML definition file: param name=history_id display=radio type=drill_down dynamic_options=vdb_init_tool_user(__trans__) / ... code file=versioned_data_form.py / Not sure if making history_id a hidden field would work (I seemed to recall __trans__ variable only exposed to select param). And in a script named versioned_data_form.py we have: def vdb_init_tool_user(trans): ... ALSO: squeezing history_id in this way since no other way to pass it. trans is provided only by tool form presentation via code file=... ... history_id = str(trans.security.encode_id(trans.history.id)) items = [ { 'name': 'think of something to say here', 'value': history_id, 'options':[], 'selected': True } ] return items ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] find UUID of current history in tool XML wrapper?
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 platform for creativity (everything exposed in case someone might find use for it). d. Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada From: Ben Bimber [bbim...@gmail.com] ... If I'm already using non-public APIs to get the current history ID, can it be done more directly using something analogous to the above? Thanks, Ben ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] find UUID of current history in tool XML wrapper?
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 state permissions). So I'm thinking John's solution is copacetic because it expresses that we're after a piece of information about the current process - where it is delivering its output - since we have other immediate processes that need to contribute to that work. Thanks for your attention in revisiting this matter! d. Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada From: Dannon Baker [dannon.ba...@gmail.com] ... Subject: Re: [galaxy-dev] find UUID of current history in tool XML wrapper? Galaxy's API goal is to be intentionally stateless, and methods that operate on a history accept that as a parameter and don't recognize the notion of 'current'. State like that is to be maintained in the client, whatever that is -- whether a webpage, cron job, etc. I think this approach is probably *more* flexible in that we don't box ourselves into relying on the notion of a 'current' history, though some few methods might currently rely on it. It's worth noting that this argument has conspicuous parallels to the argument against allowing tools to understand the 'current' history as well. ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Comment on Training Documentation
Hi, Ok, thanks for all the quick feedback folks, and your tool links John. So much work rolling off everyone's presses! John, on command and nixing interpreter= : Ok, I like that, to change it so that people can see command tag is a place for shell interaction. Re. Update / Revision distinction: So looking at this in detail (Peter and Martin ;) ) - it turns out the update and revision terms are actually from Install latest revision vs Get updates options that occur in the Galaxy interface (you can see from snapshots I did of galaxy admin view in tool versioning tutorial) when downloading tool updates. So my definitions were an attempt to explain the difference there. Perhaps then we should have a ticket to have Galaxy force any toolshed update to have a version id that increments, then no opportunity for confusion, and no need for update phrase in galaxy UI? In tutorial I do want to show people the implications of not incrementing. ... 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 don't do anything different. Advice is to encourage the dev to batch their changes into just a few revisions per year say for main Galaxy toolshed. I've downgraded this whole update thing to just say its possible to upload a change without version increment but not advisable for main toolshed. Cheers, Damion P.s. for the ffp_phylogeny tool I wanted to do piping in the command tag e.g. commandprogx -a | progy -b -c | progz/command. Easy enough unless one wants to catch errors when they happen within the piped processes. I found that verbatim one would unfortunately never see any error info from earlier stages of the pipe on return to Galaxy, right?. I took a stab at writing a check_output(command) call in ffp_phylogeny tool that sets up error reporting for each stage of pipe, which seems to do ok (though only tested manually), but wondering if anyone else has tackled the piping error reporting? Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada From: John Chilton [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. I recently created a wiki page just with tool development resource links https://wiki.galaxyproject.org/Develop/ResourcesTools that now gets embedded in other more common landing pages including https://wiki.galaxyproject.org/Admin/Tools/AddToolTutorial https://wiki.galaxyproject.org/Develop I have added links to your content from to this resource list. One quick thought on the content. The interpreter=python idiom for wrappers has been around for years and is used widely but it has some serious drawbacks - in particular nothing can come before the wrapper in the tool XML - no cheetah directives like #import or #set and no linking in files (for instance the following setup idiom: ln -s ${input_bam} temp_input.bam ln -s ${input_bam.metadata.bam_index} temp_input.bam.bai actual_command --args In the planemo documentation I am not going to mention interpreter for this reason - I think it is frustrating for people when it does not work the way intuitively it should. The forthcoming 15.03 injects a new variable called $__tool_directory__ that I think should be the new best practice. ln -s ${input_bam} temp_input.bam ln -s ${input_bam.metadata.bam_index} temp_input.bam.bai python $__tool_directory__/wrapper.py --args I understand that it might be best to not base your tutorial on features not even released yet :) - but I did want to take the opportunity to mention this idiom. As you mentioned I have also been working on updated tool development documentation lately at (http://planemo.readthedocs.org/en/latest/). I am trying to build a set of smaller resources that can be composed into tailored resources (e.g. build tools without planemo, with planemo, with planemo virtual appliance), (normal tutorial, verbose tutorial, slide-based tutorial), (with and without Docker). I don't know if rst is up to this task, but we will see. Another effort along these lines worth checking out is Kyle's tool tutorial - https://github.com/kellrott/galaxy-tooldev-docs/tree/master/docs. This tutorial is focused on using the planemo appliance and Dockerizing tools. -John On Fri, Mar 13, 2015 at 4:35 AM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Mar 13, 2015 at 12:23 AM, Martin Čech mar...@bx.psu.edu wrote: Your tutorial looks great Damion! Thank you
Re: [galaxy-dev] Tool param type library_data (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 enctype=application/x-www-form-urlencoded input type=hidden name=refresh value=refresh/ input type=hidden name=tool_id value=bccdcSelectSubsets/ input type=hidden name=tool_state value=3865326638 1323033303764 input type=hidden name=input value=4246/ input type=hidden name=incl_excl value=1/ ... and then on to the visible fields. Currently one of my galaxy tools blast_reporting generates an html report (form) which users can view and select items and submit - which calls another tool with just the right parameters, as above, including tool_state value which is copied once from viewing source of the live target tool form. 2nd tool immediately generates the desired dataset. I know html form approach is a hack but it works and it keeps things simple (its never part of a workflow). However, a nice feature for the new tool form engine would be to have the tool state accept an empty value= for initial submission of forms. Is that possible? That way I wouldn't have to bother with one other yucky installation step for my blast_reporting tool where one has to manually view source of an instance of the target tool (bccdcSelectSubsets above) and retrieve the generic tool_state field value setting. d. ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool Testing: field inputs that occur inside repeat tag - resolved
Yay, with your tip, galaxy direct tests now work with tool_conf.xml AND data table in place! Galaxy DOC person: please update https://wiki.galaxyproject.org/Admin/RunningTests to state that tool_conf.xml.sample is NOT used for testing! It is stated in the run_tests.sh help info half way down the page. Tool wasn't loading on new site because data table it referenced wasn't set up. I'll note for galaxy devs that the WARNING is actually fatal i.e. that missing data table caused some kind of weird error: galaxy.tools.toolbox.base INFO 2015-02-27 13:48:48,190 Parsing the tool configuration ./config/tool_conf.xml galaxy.tools.parameters.dynamic_options WARNING 2015-02-27 13:48:48,199 Data table named 'blast_reporting_fields' is required by tool but not configured galaxy.tools.toolbox.base ERROR 2015-02-27 13:48:48,200 Error reading tool from path: TESTING/blast_reporting/blast_reporting.xml Traceback (most recent call last): File ...galaxy-dist/lib/galaxy/tools/toolbox/base.py, line 670, in _load_tool_tag_set tool = self.load_tool( os.path.join( tool_path, path ), guid=guid, repository_id=repository_id ) ... File .../galaxy-dist/lib/galaxy/tools/parameters/dynamic_options.py, line 608, in column_spec_to_index return int( column_spec ) ValueError: invalid literal for int() with base 10: 'type' Thanks again, Peter! Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, 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. ... And I run tests.sh -id blast_reporting (with Galaxy as owner of tool folder): While the tests used to use tool_conf.xml.sample last year (or even longer ago?) this was switched to using the main tool_conf.xml instead. This is much easier for testing what you actually have installed. If I've guessed wrong, watch the run_tests.sh output to see which tools are loaded - and make sure your tool loads OK (and for example doesn't fail with an XML error or something). 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] FW: Tool Testing: field inputs that occur inside repeat tag
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 ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool Testing: field inputs that occur inside repeat tag
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, but has no legal values defined requests.packages.urllib3.connectionpool: DEBUG: POST /api/tools HTTP/1.1 500 None I presume its because of extra stuff needed to name variables have to be referred-to when they are inside a repeat section? Or is it just something pecular to do with data_table_sources? test!-- Equivalent to output of old bccdc BLASTn XML to Tabular -- param name=blastxml_file value=blast_reporting_1.blastxml/ output name=tabular_file file=blast_reporting_1a.tabular/ param name=out_format value=std/ param name=column_labels value= / param name=drop_redundant_hits value=true/ /test test param name=blastxml_file value=blast_reporting_1.blastxml/ output name=tabular_file file=blast_reporting_1b.tabular/ param name=out_format value=std/ param name=column_labels value= / param name=drop_redundant_hits value=true/ param name=filter_column value=pident/ param name=filter_comparison value=gte/ param name=filter_value value=97/ /test The form repeat area: repeat name=filter_num title=Numeric Filter min=0 max=4 param name=filter_column type=select label=Col options from_data_table=blast_reporting_fields filter type=static_value value=numeric column=type / filter type=sort_by column=name/ /options /param repeat name=constraint title=Constraint min=1 max=3 param name=filter_comparison type=select label=Comparison option value=gtegt;= /option option value=gtgt;/option option value=ltlt; /option option value=ltelt;= /option option value===equal to /option option value=!=not equal to /option /param param name=filter_value type=text value= label=Value validator type=regex message=Please input a number([0-9]+|[0-9]*\.[0-9]+)/validator /param /repeat /repeat The working command section that sends the filter field info is: #for $i, $my_repeat in enumerate( $filter_num ) $my_repeat.filter_column: #for $i, $my_repeat2 in enumerate( $my_repeat.constraint ) $my_repeat2.filter_comparison $my_repeat2.filter_value, #end for ; #end for Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool test failure - I could use some help...
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 thorough checklist on issues around this? Tool xml file header: tool id=ffp_phylogeny name=Feature Frequency Profile Phylogeny version=0.1.00 Using John Chilton's ready made sqlite db (though our live server uses a postgres one) export GALAXY_TEST_DB_TEMPLATE=tmp/db_gx_rev_0120.sqlite Command line (recent Update tag latest_2015.01.13 for changeset 0cb6cec4ee57): run_tests.sh -id ffp_phylogeny begins the process alright. *** My galaxy-dist/tool_shed.xml.sample where I understand references to the tool are supposed to go (and I confirmed the tool file absolute path): ?xml version=1.0? toolbox tool_path=../shed_tools section id=bccdc_tools name=BCCDC Tools version= tool file=/usr/local/galaxy/production1/shed_tools/salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/eb1924fbd3ba/ffp_phylogeny/ffp_phylogeny.xml guid=salk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/ffp_phylogeny/0.1.00 tool_shedsalk.bccdc.med.ubc.ca/toolshed/tool_shed repository_nameffp_phylogeny/repository_name repository_ownerddooley/repository_owner installed_changeset_revisioneb1924fbd3ba/installed_changeset_revision idsalk.bccdc.med.ubc.ca/toolshed/repos/ddooley/ffp_phylogeny/ffp_phylogeny/0.1.00/id version0.1.00/version /tool tool file=salk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/e9ebe2959300/versioned_data/versioned_data.xml guid=salk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/versioned_data/0.1.00 tool_shedsalk.bccdc.med.ubc.ca/toolshed/tool_shed repository_nameversioned_data/repository_name repository_ownerdamion/repository_owner installed_changeset_revisione9ebe2959300/installed_changeset_revision idsalk.bccdc.med.ubc.ca/toolshed/repos/damion/versioned_data/versioned_data/0.1.00/id version0.1.00/version /tool /toolbox Thanks for any pointers! Soon as tests fly, I'll be contributing the tools up to the test tooshed. Regards, Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool param type library_data (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 galaxy dev can tackle this, great! Otherwise I'll have to drop this approach :( * For others who may need... tool form's param: param name=library_datasets type=library_data label=Reference Bin file help=Select one reference bin at a time from the popup window's Reference Bin library./ command tag contents #if $library_datasets -B #for $i, $dataset in enumerate($library_datasets) #$dataset.get_file_name() $dataset.id #end for #end if Successfully submits either the full file path of selected dataset, or its id. * However trying to rerun this history tool item gets us an error (not related to the above command contents): Error Traceback: View as: Interactive | Text | XML (full) ⇝ AttributeError: 'int' object has no attribute 'id' Module galaxy.tools.parameters.basic:146 in value_to_basic view return self.to_string( value, app ) Module galaxy.tools.parameters.basic:2406 in to_string app galaxy.app.UniverseApplication object at 0x59a0710 ldda331 selfgalaxy.tools.parameters.basic.LibraryDatasetToolParameter object at 0x7fced01d2090 value [331] return [ldda.id for ldda in value] AttributeError: 'int' object has no attribute 'id' which is in /lib/galaxy/tools/parameters/basic.py: class LibraryDatasetToolParameter( ToolParameter ): Parameter that lets users select a LDDA from a modal window, then use it within the wrapper. ... def to_string( self, value, app ): if not value: return value return [ldda.id for ldda in value] Value is getting an array of dataset ids, whereas this method is expecting value to be a list of dataset objects. I tried changing ldda.id to just id but found other parts of LibraryDatasetTool code were broken as they too were expecting an object. Maybe this is related to the tool job's history detail link showing Reference Bin file as a string label of an object?: Input Parameter Value Note for rerun BLAST results as XML240: megablast Pasted Entry vs 16SMicrobial.fasta Reference Bin file [galaxy.model.LibraryDatasetDatasetAssociation object at 0x7fcee04d4350] Tabular Report Column LabelsShort name HTML Report templatetemplates.html_report The other bug: 2) Tool_form.mako has a hardcoded url that doesn't work for galaxy installs that have a prefix so that needs adjustment: $(.add-librarydataset).click(function() { var link = $(this); $.ajax({ url: /visualization/list_libraries, ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Tool param type library_data
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 that doesn't work for galaxy installs that have a prefix so that needs adjustment: $(.add-librarydataset).click(function() { var link = $(this); $.ajax({ url: /visualization/list_libraries, Now one gets the popup form in one's tool where one or more library datasets can be selected. Selecting one or more gets them listed in one's tool form. However, I'm not understanding how to get those items submitted with galaxy form command params. I tried for example: -B $library_datasets[0].file_name and also tried a loop to enumerate the dataset file names. I keep on getting: File cheetah_DynamicallyCompiledCheetahTemplate_1421706558_2_37415.py, line 203, in respond TypeError: object of type 'LibraryDatasetValueWrapper' has no len() If anyone knows the solution, that would be appreciated. Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Tool param type library_data
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 date:2011-07-19 03:56:23 summary: Tools: Add new LibraryDataset tool parameter to expose LDDAs to tools. Use trackster's modal popup interface for item selection. Add new InputWrapper that exposes LDDA templates as well. Now I can't quite fathom the syntax around this but it appears to be broken - python error displayed: TypeError: get_initial_value() got an unexpected keyword argument 'history' Which is because in the galaxy code the def get_initial_value( self, trans, context ) function is missing a history=None parameter like other types have?! But is this input type essentially discontinued (no other refs to it on the web) or is it supposed to be operational? I was hoping for a tool input that would list a particular libraries datasets, so that I could obtain their file paths for use in my tool. param name=test type=library_data label=test help=test help/ options library=Reference Bins /param Regards, Damion Hsiao lab, BC Public Health Microbiology Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] No API way to delete a galaxy data library folder?
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 call like: http://[my galaxy]/api/folders/[my folder id]/delete I haven't tested since I haven't played with Next-stable galaxy branch. When roughly does that get woven into stable or default? Regards, Damion Martin Čech | Threaded | More Dec 04, 2014; 4:40pm Re: No API way to delete a galaxy data library folder? I have actually implemented this feature and it will be in the next release (which should be made public around next monday). ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Galaxy Bioblend option for importing dataset into a library? (Nicola Soranzo)
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 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] No API way to delete a galaxy data library folder?
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, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___ 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: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/