Re: [galaxy-dev] bowtie dataset pair input
Hi Ryan, latest wrappers are here: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 And a PR would be great! But as far as I can see this is already implemented and you can choose as option `Paired-end Dataset Collection`, isn't it? Ciao, Bjoern On 24.06.2015 20:02, Ryan G wrote: Hi all - It looks like bowtie's wrapper is working incorrectly for a list of dataset pairs. Its expecting all the forward reads in one dataset list and the reverse reads in a separate dataset list. Instead, I have a list of dataset pairs (for paired-end data). This cannot be provided to bowtie as input. If I correct this, should I create a pull request for it? Alternatively, does someone already have a corrected version of this? ___ 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/ ___ 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] problem with view of list collection in history view
Hi Team, my tool creates dynamically 96 datasets bundled into a list. In the history I can see the number 96 in the top as hidden datasets (6 shown, 96 hidden) When I open the list, I just can see 64 items. Now I run the job again and I have 96 more hidden items. I open the new list and can see 66 items in that new list. What is going on here? Is that just a visual bug? Or are my datasets affected? Thanks, Alexander PS: I use postgres ___ 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] list collection output - format set from input
no - not a typo. The tool can process both.
It's just my naming, because I use it for fastq.
I'll change the help tag.
2015-06-25 3:44 GMT-05:00 Peter Cock p.j.a.c...@googlemail.com:
Hi Alexander,
If this wasn't a collection, I would expect format_source to work
(possibly also using metadata_source=fastq_input1), so perhaps
this is a bug - John?
Peter
P.S. Your help caption and output label both say FASTQ, but the
input also allows FASTA input. Typo?
On Thu, Jun 25, 2015 at 2:39 AM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
Hi,
I have an input, that can be fasta,fastqsanger,fastqillumina:
param name=fastq_input1 type=data
format=fasta,fastqsanger,fastqillumina label=Select the fastq file
help=Specify fastq file with reads/
I have multiple outputfiles - bundled in a list collection:
collection name=split_output type=list label=@OUTPUT_NAME_PREFIX@
on
${on_string} (Fastq Collection) format_source=fastq_input1
discover_datasets pattern=__name_and_ext__ directory=splits /
/collection
The format_source parameter doesn't work - the files in the list
(extension
fq) are of format fq
How can I make it possible that they are fasta,fastqsanger,fastqillumina
depending on fastq_input1?
Thanks,
Alexander
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Re: [galaxy-dev] list collection output - format set from input
Hi John,
yes - I created this hacky solution and it works.
I now tried what you said, but no success.
Code:
collection name=split_output type=list label=@OUTPUT_NAME_PREFIX@
on ${on_string} (Fastq Collection) format_source=fastq_input1
discover_datasets pattern=sample_(?Plt;namegt;.+)\.fq
directory=output /
/collection
It puts the samples into the collection correctly, but doesn't set a data
type.
Weird enough: In the collection, the files even don't show any format
(in the small history view on the right). Is that normal?
Addon: How can I let the files in the collection have the same database
build
attached? The other file (log file) gets it.
Best,
Alexander
2015-06-25 9:12 GMT-05:00 John Chilton jmchil...@gmail.com:
You are giving Galaxy mixed signals :). format_source will say to use
the data type specified by the corresponding input - but
discover_datasets pattern=__name_and_ext__ directory=splits /
Is saying (with the pattern __name_and_ext__) read files of the form
out1.fastq and assign the collection identifier to out1 and the
extension/format to fastq.
Two things should work - one of them will and the other might but should.
One thing you can do is not override the extension in your pattern:
discover_datasets pattern=__name__ directory=splits /
or if you don't want to include the .fq in the output identifier (and
you probably don't want to)
discover_datasets pattern=(?Plt;namegt;.+)\.fq /
If that doesn't work - it is a bug and please let me know and I will
attempt to fix it.
The hackier way to get this to work that I am more confident will work
- is to drop the format_source - use the same pattern:
discover_datasets pattern=__name_and_ext__ directory=splits /
But just use a shell command or something to rename all files of the
form *.fq to *.${fastq_input1.ext}.
Hope this helps.
-John
On Thu, Jun 25, 2015 at 9:56 AM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
no - not a typo. The tool can process both.
It's just my naming, because I use it for fastq.
I'll change the help tag.
2015-06-25 3:44 GMT-05:00 Peter Cock p.j.a.c...@googlemail.com:
Hi Alexander,
If this wasn't a collection, I would expect format_source to work
(possibly also using metadata_source=fastq_input1), so perhaps
this is a bug - John?
Peter
P.S. Your help caption and output label both say FASTQ, but the
input also allows FASTA input. Typo?
On Thu, Jun 25, 2015 at 2:39 AM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
Hi,
I have an input, that can be fasta,fastqsanger,fastqillumina:
param name=fastq_input1 type=data
format=fasta,fastqsanger,fastqillumina label=Select the fastq file
help=Specify fastq file with reads/
I have multiple outputfiles - bundled in a list collection:
collection name=split_output type=list
label=@OUTPUT_NAME_PREFIX@
on
${on_string} (Fastq Collection) format_source=fastq_input1
discover_datasets pattern=__name_and_ext__ directory=splits
/
/collection
The format_source parameter doesn't work - the files in the list
(extension
fq) are of format fq
How can I make it possible that they are
fasta,fastqsanger,fastqillumina
depending on fastq_input1?
Thanks,
Alexander
___
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Re: [galaxy-dev] list collection output - format set from input
You are giving Galaxy mixed signals :). format_source will say to use
the data type specified by the corresponding input - but
discover_datasets pattern=__name_and_ext__ directory=splits /
Is saying (with the pattern __name_and_ext__) read files of the form
out1.fastq and assign the collection identifier to out1 and the
extension/format to fastq.
Two things should work - one of them will and the other might but should.
One thing you can do is not override the extension in your pattern:
discover_datasets pattern=__name__ directory=splits /
or if you don't want to include the .fq in the output identifier (and
you probably don't want to)
discover_datasets pattern=(?Plt;namegt;.+)\.fq /
If that doesn't work - it is a bug and please let me know and I will
attempt to fix it.
The hackier way to get this to work that I am more confident will work
- is to drop the format_source - use the same pattern:
discover_datasets pattern=__name_and_ext__ directory=splits /
But just use a shell command or something to rename all files of the
form *.fq to *.${fastq_input1.ext}.
Hope this helps.
-John
On Thu, Jun 25, 2015 at 9:56 AM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
no - not a typo. The tool can process both.
It's just my naming, because I use it for fastq.
I'll change the help tag.
2015-06-25 3:44 GMT-05:00 Peter Cock p.j.a.c...@googlemail.com:
Hi Alexander,
If this wasn't a collection, I would expect format_source to work
(possibly also using metadata_source=fastq_input1), so perhaps
this is a bug - John?
Peter
P.S. Your help caption and output label both say FASTQ, but the
input also allows FASTA input. Typo?
On Thu, Jun 25, 2015 at 2:39 AM, Alexander Vowinkel
vowinkel.alexan...@gmail.com wrote:
Hi,
I have an input, that can be fasta,fastqsanger,fastqillumina:
param name=fastq_input1 type=data
format=fasta,fastqsanger,fastqillumina label=Select the fastq file
help=Specify fastq file with reads/
I have multiple outputfiles - bundled in a list collection:
collection name=split_output type=list label=@OUTPUT_NAME_PREFIX@
on
${on_string} (Fastq Collection) format_source=fastq_input1
discover_datasets pattern=__name_and_ext__ directory=splits /
/collection
The format_source parameter doesn't work - the files in the list
(extension
fq) are of format fq
How can I make it possible that they are fasta,fastqsanger,fastqillumina
depending on fastq_input1?
Thanks,
Alexander
___
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Re: [galaxy-dev] Using API to identify all datasets that were part of a workflow?
the latter. starting with a dataset, pull it's full history. therefore if it was created by running a simple single-step tool it's one step. if it was created as part of a workflow, grab that whole series of steps/inputs/outputs. i agree on the python/java bindings being out of date, but even when i was scanning the JSON I wasnt able to see where I'd glean this information. the missing thing for me was always determining if a given dataset was connected to a larger workflow. -ben On Thu, Jun 25, 2015 at 7:26 AM, John Chilton jmchil...@gmail.com wrote: Can you clarify one thing for me - are you attempting to break a workflow invocation into steps, and then jobs, and then inputs and outputs (so working from the workflow invocation) or are you trying to scan existing histories and find a workflow for each dataset (so working from the history id and workflow id maybe)? I feel like this should be doable now - though blend4j and to a lesser extent even bioblend are pretty far behind what I would consider best practices for invoking workflows via the API so they may need to be updated. -John On Thu, Jun 25, 2015 at 10:04 AM, Ben Bimber bbim...@gmail.com wrote: Hello, I'm still relatively new to galaxy. I'm trying to use the API to identify the string of jobs/datasets that were created as part of executing a workflow. So far as I can tell, the API gives me the ID of the job, which corresponds to one step in the workflow. Each of these has inputs/outputs. I can walk outwards and try to connect any other jobs that happen to use one of these files as an input or output; however, I am not seeing any key that provides a more direct indication that a set of steps was executed as part of a given workflow. Am I missing something? Thanks in advance, 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/ ___ 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] Using API to identify all datasets that were part of a workflow?
Can you clarify one thing for me - are you attempting to break a workflow invocation into steps, and then jobs, and then inputs and outputs (so working from the workflow invocation) or are you trying to scan existing histories and find a workflow for each dataset (so working from the history id and workflow id maybe)? I feel like this should be doable now - though blend4j and to a lesser extent even bioblend are pretty far behind what I would consider best practices for invoking workflows via the API so they may need to be updated. -John On Thu, Jun 25, 2015 at 10:04 AM, Ben Bimber bbim...@gmail.com wrote: Hello, I'm still relatively new to galaxy. I'm trying to use the API to identify the string of jobs/datasets that were created as part of executing a workflow. So far as I can tell, the API gives me the ID of the job, which corresponds to one step in the workflow. Each of these has inputs/outputs. I can walk outwards and try to connect any other jobs that happen to use one of these files as an input or output; however, I am not seeing any key that provides a more direct indication that a set of steps was executed as part of a given workflow. Am I missing something? Thanks in advance, 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/ ___ 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] Data Collections
For the list sake - I think we figured this out and IRC and it had to do with having two versions of Galaxy installed on the same machine. Alexander - let me know if this issue is not resolved. -John On Mon, Jun 15, 2015 at 4:02 PM, Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Thank you for this detailed descriptions! I already have a followup question. I'm working on Galaxy Cloudman: Galaxy is at revision: 93cda3eb81 (master branch) from 11 Jun 2015) But I just can find Build dataset pair|list, not List of Dataset Pairs like in the video. At what version is that implemented? Best, Alexander 2015-06-15 10:17 GMT-05:00 John Chilton jmchil...@gmail.com: On Wed, Jun 10, 2015 at 4:04 PM, Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Hi Folks, thank you so far for the previous help. I got much further. Now I'm stuck with data collections. Because this is quite a list, I appreciate also answers to parts of my questions ;) I have two issues: A) manual definition of data collections (any type) by user and/or admin B) definition of data collections as input/output of a tool and inside a workflow A) manual Basically I would like to create i) a list of fastq files (unpaired) ii) a paired set of two fastq files iii) a list of each two paired fastq files How can I do that? By using the web app? As user? As admin? By working via ssh on the server? So each of these got much easier/more robust with the most recent release. For the user perspective - for any of these options you will want to load the fastq files into a history, open the manage multiple datasets option (https://wiki.galaxyproject.org/Histories#Managing_Multiple_Datasets_Easily), select the datasets, and then choose the list type from the menu. Each will cause a widget to pop up allowing you to group the datasets (into a list, a pair, or a list of pairs depending on your selection). The most complicated option is the list of pairs - this option is demonstrated in a the first video in Anton's recent NGS 101 - Reference-based RNA-seq series (https://vimeo.com/channels/884356/128265983). More information at https://wiki.galaxyproject.org/Learn/GalaxyNGS101. For all user-centric scenarios - you will need to get the plain datasets into a history first. FTP upload for instance doesn't support creating collections directly - you can import datasets and then create them. Likewise - data libraries do not currently support dataset collections. I believe there are Trello cards for both of these issues. For admins - there is a dataset collection API - I can point you at examples if you want - but this doesn't seem to be your interest. B) in tool/workflow Here I also have different approaches I would like to realize: i) use a collection as input for a tool ii) create a collection as output of a tool ii.1) from known # of output parameters ii.2) from unknown # of output parameters For these things I was trying to find some tools in toolshed to see how they do it, but I couldn't quite adopt it. I would look in the following directory instead of the tool shed - https://github.com/galaxyproject/galaxy/tree/dev/test/functional/tools. These are the tools used to drive the testing of the collections implementation and contain some very stripped down examples of what is possible. i) use a collection as input for a tool this is good documented - realizable by type=data_collection and the collection_type. Unfortunately I can't test this because I can't create a collection so far ;) - see A Indeed :). Here some good examples are like the tools in the RNA-seq pipeline - Tophat, Bowtie2, etc ii) create a collection as output of a tool Here it gets blurry for me. So one can get very far without ever creating an output from a tool explicitly. I contend most of the time - if you have a list of bam files and you want to create another list of bam files - you just want to map some operation over them. This is demonstrated in that RNA-seq outline - and talked about in a more theoretical way in my GCC talk from last year http://bit.ly/gcc2014workflows. There are definitely cases when you want to explicitly create collections though - the current best documentation on this is going to be the pull request that added them - not the implementation but the description which actually lays out these same categories and how to handle them with explicit complete examples. https://bitbucket.org/galaxy/galaxy-central/pull-request/634/allow-tools-to-explicitly-produce-dataset Hopefully this helps - please follow up with additional questions as you have them. I am keen to see more developers leveraging dataset collections. Thanks a bunch. -John ii.1) from known # of output parameters Here I didn't find a tool. I just thought, it might be a simpler case than ii.2 and good to understand the concept.
[galaxy-dev] Using API to identify all datasets that were part of a workflow?
Hello, I'm still relatively new to galaxy. I'm trying to use the API to identify the string of jobs/datasets that were created as part of executing a workflow. So far as I can tell, the API gives me the ID of the job, which corresponds to one step in the workflow. Each of these has inputs/outputs. I can walk outwards and try to connect any other jobs that happen to use one of these files as an input or output; however, I am not seeing any key that provides a more direct indication that a set of steps was executed as part of a given workflow. Am I missing something? Thanks in advance, 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] bowtie dataset pair input
What Bjoern said - unless you meant the older bowtie1 wrappers. Those have not been updated - I think we decision was made at Penn State to focus on bowtie2 - but if people are still interested in enhancing the bowtie1 wrappers I think a PR would be welcome. There have been some other relatively recent bowtie1 PRs (e.g. from Nicola https://github.com/galaxyproject/tools-devteam/pull/49). -John On Thu, Jun 25, 2015 at 3:46 AM, Bjoern Gruening bjoern.gruen...@gmail.com wrote: Hi Ryan, latest wrappers are here: https://github.com/galaxyproject/tools-devteam/tree/master/tools/bowtie2 And a PR would be great! But as far as I can see this is already implemented and you can choose as option `Paired-end Dataset Collection`, isn't it? Ciao, Bjoern On 24.06.2015 20:02, Ryan G wrote: Hi all - It looks like bowtie's wrapper is working incorrectly for a list of dataset pairs. Its expecting all the forward reads in one dataset list and the reverse reads in a separate dataset list. Instead, I have a list of dataset pairs (for paired-end data). This cannot be provided to bowtie as input. If I correct this, should I create a pull request for it? Alternatively, does someone already have a corrected version of this? ___ 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/ ___ 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/ ___ 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] samtools dependency changes ?
Hi Wolfgang, I only can tell you that we also have problems with handling BAM files properly in Galaxy. Our issue is more due to unsorted BAM files, but as far as I understood this is because the metadata creation changed from using samtools to using pysam. Maybe this helps you in finding a workaround. Ciao, Bjoern hmm, no replies yet, so is anybody able to reproduce this behavior and would you not consider it a bug? Best, Wolfgang On 06/16/2015 03:11 PM, Wolfgang Maier wrote: Dear all, with older Galaxies (prior to latest_15.03 I think), you could satisfy Galaxy's samtools dependence for indexing bam files by having a samtools executable in tool-dependencies/samtools/default/bin (with the tool-dependencies directory declared as tool_dependency_dir in galaxy.ini of course). Now (checked with latest_15.03 and .05), this is not working any more! The executable will still be used during bam uploads, but not when a bam file gets created by a tool. The reason is that before the job runner (tested this with the local job runner only) used to build the dependency shell command for dependency 'samtools' before finishing a job, but now the job wrapper finish method fails because it naively expects to find samtools on $PATH. Best, Wolfgang ___ 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/ ___ 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/ ___ 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] input dataset(s) and collections
If the user selects mulitple pairs of paired-end data, I want that submitted the same way as a list of paired-end data. I don't want a separate job for each paired-end data. Rather, I want a single job to consume the entire list. It seems to be easier to disable the ability to select multiple fastq1s and fastq2s, and only allow the user to specify a list of paired-end reads. This way, I can guarantee the pairs of fastq files match up correctly. On Thu, Jun 25, 2015 at 10:41 AM, John Chilton jmchil...@gmail.com wrote: So you don't want the multi-run options to appear next to these inputs? There is currently no way for the tool author to disable this. I will admit that I am skeptical this is a good idea, fundamentally is feels like tool authors should not be able to prevent end users from running the tool multiple times in parallel. Though I will also admit in practice there are times this option leads to confusion for users about what will actually happen and multiple people have requested an option to disable it. http://dev.list.galaxyproject.org/Tool-development-Selecting-a-single-item-from-input-dataset-td4666447.html https://trello.com/c/qCtBBB8n -John On Tue, Jun 23, 2015 at 12:58 PM, Ryan G ngsbioinformat...@gmail.com wrote: Hi all - I'm constructing a wrapper for a tool I have and the input to the tool can be: 1) a single fastq file (single end sample) 2) multiple singled-end fastq files 3) a single paired-end sample 4) multiple paired-end samples. I have cases #1 and #2 handled, however case #3 is presenting a problem. If the user select Paired-End sample, I want to restrict them to selecting only a single fastq1 and fastq2 file. If they want to submit multiple paired-end samples I only want to allow them to submit them as a list of dataset pairs. I can get this part to work. I just need to restrict users to selecting only a single fastq1 and fastq2 file when the input_type is Paired-End. My XML is as follows. Any help would be appreciated !-- Input FastQ file(s) -- conditional name=input_type param name=input_type_selector type=select label=Select input type help=Select between single and paired fastq data option value=singleSingle-End/option option value=pairedPaired-End/option option value=paired_collectionPaired Collection/option /param when value=single param name=fastq_input1 type=data format=fastq label=Select fastq dataset multiple=true help=Specify dataset with single end reads / /when when value=paired param name=fastq_input1 type=data format=fastq label=Select fastq dataset help=Specify dataset with 1st of paired-end reads / param name=fastq_input2 type=data format=fastq label=Select fastq dataset help=Specify dataset with 2nd of paired-end reads / /when when value=paired_collection param name=fastq_collection type=data_collection collection_type=list:paired label=Select a paired collection help=See help section for an explanation of dataset collections/ /when /conditional ___ 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/ ___ 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] problem with view of list collection in history view
Conversation in IRC. tl;dr - it looks like it might be a GUI related problem since the API does contain all of the datasets. Carl - any chance you have an idea of what is going on here? 21:20 jmchilton avowinkel: is it possible there were duplicated identifiers (has your discover_datasets pattern changed from earlier) 21:21 jmchilton I'm leaning toward saying it is likely a backend problem - since explicit output collections are pretty new and you are the first person I can think of really exercising them strenuously 21:21 jmchilton One way to verify though is to check the API - if you just open localhost:port/api/histories in your browser - find the history id 21:21 jmchilton then open /api/histories/history_id/contents and then find the collection 21:22 jmchilton you should be able to open something like 21:22 jmchilton /api/histories/history_id/contents/collections/collection_id - which should show the individual datasets 21:23 avowinkel there are defenitely no duplicate designations - if thats the same like identifiers 21:23 avowinkel It's still discover_datasets pattern=__name_and_ext__ directory=splits / 21:27 jmchilton My next question would be (if you can verify it is a backend thing) - are the elements in the dataset - the hidden elements less than a certain HID - or are they random. 21:28 avowinkel via the api all 96 entries are in the collection 21:29 avowinkel with element_index's 0 to 95, in total 96 21:29 avowinkel in both lists 21:31 avowinkel biggest hid is 202 21:32 avowinkel the parent's list hid is always smaller than the containing element's hids 22:26 jmchilton so you are sure every element_index from 0 to 95 is represented? This being a GUI problem is really odd - but it seems like it probably is. I wonder if someone a div id is generated from the identifiers in such a way that one is duplicated. Seems unlikely 22:26 jmchilton Can you open your JavaScript console and see if there are any JavaScript errors/ 22:27 avowinkel well. I did grep element_index, I saw index 0 on the top, Index 95 on the bottom. and wc -l gives 96 - so yes. very sure 22:28 avowinkel and when I scan loosely through the list of greps, I don't see anything odd 22:29 avowinkel don't want to count from 0 to 95 ^^ 22:29 jmchilton :) 22:29 avowinkel for all the tests 22:30 jmchilton does that API response have a hidden field for the datasets? 22:31 avowinkel there is nothing in that file that matches hidden 22:31 avowinkel (in the history they are all hidden) 22:32 jmchilton I would open your web browser and check for javascript errors next 22:34 avowinkel nop. nothing (Firefox 34 - ubuntu biolinux) 22:34 jmchilton can you send me a screenshot of the expanded collection? 22:35 avowinkel the newest run has 69 entries in the history 22:36 avowinkel what part do you want screenshotted? 22:38 jmchilton When I open the list, I just can see 64 items. The opened list in the history panel 22:40 avowinkel http://snag.gy/2knoI.jpg 22:43 jmchilton are you hand counting these lists in the browswer then? 22:47 avowinkel yes, hand counting 22:50 jmchilton I'll ping carl about this - he is the GUI mastermind - he might have some clue 22:59 avowinkel jmchilton: http://pastebin.com/DcpF1QAU 22:59 mrscribe Title: [YAML] galaxy dataset_collection contents - Pastebin.com (at pastebin.com) 23:00 avowinkel don't get confused: On the picture is a different dataset. It doesn't have sample_ in the name 23:04 jmchilton yeah - that response looks perfectly fine - really odd -John On Thu, Jun 25, 2015 at 4:58 PM, Alexander Vowinkel vowinkel.alexan...@gmail.com wrote: Hi Team, my tool creates dynamically 96 datasets bundled into a list. In the history I can see the number 96 in the top as hidden datasets (6 shown, 96 hidden) When I open the list, I just can see 64 items. Now I run the job again and I have 96 more hidden items. I open the new list and can see 66 items in that new list. What is going on here? Is that just a visual bug? Or are my datasets affected? Thanks, Alexander PS: I use postgres ___ 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/ ___ 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/
