- galaxy-dev - lists.galaxyproject.org

custom builds as tool in toolbox panel?
by Michal Stuglik 07 Jul '11

07 Jul '11

hi, Would it be possible to build in a "Custom builds" form user menu to toolbox panel as a tool? Now it is not possible to use this feature in workflow ( as a part of pipeline)... all the best, michal

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suggestions for the SAM-to-BAM tool
by Assaf Gordon 07 Jul '11

07 Jul '11

Hi, Couple of things that can be slightly improved in the SAM-to-BAM tool: 1. "Reference list" is not informative (it's the technical way to say: "list of chromosomes and their sizes based on a FASTA file"). Users do not generally know what "reference list" is. 2. The "Locally Cached" option is not informative (I had to look in the source code to understand what it means). What it should say is something like: "Get list of chromosomes/sizes based on the dataset's organism/database" (could be shorter, but should be friendly enough). 3. There's no option of having the chromosome list in the SAM file header. Some SAM files will contain the header (can even be done in the standard bowtie tool wrapper) - saves the need to specify where to get the "reference list" from. 4. Autodetection in the "set-metadata" step will go a long way here: if the SAM file already have a header, then no need to even ask about it. If it doesn't have a header but have a DBKEY, then we're still OK. If no DBKEY and no header, then complain or ask for a FASTA file from current history. (I realize the implementing this feature is hard and annoying, I don't imply that it's easy to do, just that it's needed). 5. Inside the python script (sam_to_bam.py) there's a comment that says: "for some reason the samtools view command gzips the resulting bam file without warning" . Not sure why one cares about that, but "samtools view -u" will output an uncompressed BAM file. 6. samtools support piping, so a lot of I/O (and some time) can be spared by piping the two commands together: samtools view -u -b -S "INPUT.SAM" | samtools sort - OUTPUT Instead of running two commands and generating a temporary unsorted BAM file. -gordon

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rgWebLogo3 with Probabilities instead of Entropy
by Assaf Gordon 07 Jul '11

07 Jul '11

Hello Ross and Galaxy team, May I suggest this small patch, that enables WebLogo to plot either Entropy bits (the current default) or just nucleotides probabilities ? It uses the standard "-U" parameter of "weblogo3". -gordon

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Re: [galaxy-dev] Several errors from run.sh
by charlie 07 Jul '11

07 Jul '11

> Hi all, > > I am upgrading to the most recent galaxy-dist 720455407d1c<https://bitbucket.org/galaxy/galaxy-dist/changeset/720455407d1c> > . > First time run.sh shows following errors as in attachment. > It seems when I use 'manage_db.sh upgrade' it doesn't create necessary > tables for these tools. > Wonder if these are known issues? > > Thanks > > >

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Re: [galaxy-dev] [galaxy-user] double login / deleting users
by Nate Coraor 07 Jul '11

07 Jul '11

Joseph Hargitai wrote: > > Hi, > > 1, > referencing old thread: > http://gmod.827538.n3.nabble.com/Deleting-accounts-td867222.html > > is the delete functionality still status-quo? i.e - there is no delete other than the workaround? Hi Joe, Since this is regarding a local installation, I've moved this thread to the galaxy-dev list. I believe you still need the workaround, yes. > 2, > switched from SQLlite to postgres and have this strange double login issue. Included image - need to login twice and logout twice. Double tab - By any chance, are you using require_login = True in the config? Which logout link are you clicking to get to that page? Thanks, --nate > > joe > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/

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adding qseq2fastq tool to the main instance
by Mete Civelek 07 Jul '11

07 Jul '11

Hi, Is it possible to add the qseq2fastq tool developed by vipints (found under repositories) to the Galaxy web portal (the central server, not my own instance of Galaxy)? I believe this would be a popular tool used by many Illumina users? Best Regards, Mete Civelek ________________________________ IMPORTANT WARNING: This email (and any attachments) is only intended for the use of the person or entity to which it is addressed, and may contain information that is privileged and confidential. You, the recipient, are obligated to maintain it in a safe, secure and confidential manner. Unauthorized redisclosure or failure to maintain confidentiality may subject you to federal and state penalties. If you are not the intended recipient, please immediately notify us by return email, and delete this message from your computer.

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Bam to fastq
by Zschunke, Aaron M. 07 Jul '11

07 Jul '11

Hi, Is there any way to convert a certain section of a bam file to fastq using the galaxy tools? I just want to convert a certain part of the genome. Thanks. Aaron

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Cleanup scripts - question or bug ?
by Assaf Gordon 06 Jul '11

06 Jul '11

Hi, I'm trying to use the built-in cleanup scripts (instead of my own), came across a possible bug: 1. When running "delete_datasets.sh", the "info_only" flag is ignored. This is evident by running it twice with "-i" and getting different results (the second time - no datasets are deleted). 2. When running "purge_datasets.sh" with the "info_only" flag, no information is printed at all, making it impossible to know what would be purged without the "-i" flag. The only way to see what is purged is actually purging the datasets (kind of defeats the purpose of "info only"). I think the attached patch fixes both issues. 3. The relevant wiki page (https://bitbucket.org/galaxy/galaxy-central/wiki/Config/PurgeHistoriesAndDa…) says about "delete_datasets.sh": "The purge_datasets.sh script will need to be run afterwards to remove the base datasets from disk." But the example on the wiki page (and in the script) has "-r" - so the files are actually deleted from the disk by "delete_datasets.sh". Does one still need to run "purge_datasets.sh" if used "-r" with "delete_datasets.sh" ? 4. If I accidentally run "purge_datasets.sh" without "-r" = is there a way to delete the stale files ? if not, perhaps the script should require either "-i" or "-r" to avoid such cases (or provide another cleanup script?) comments are welcomed, -gordon

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New Tool Shed: Inconsistent field names
by Peter Cock 06 Jul '11

06 Jul '11

Hi all, I've noticed some inconsistencies in the new tool shed. First of all the table view uses "Name" and "Description" for fields shown as "Name" and "Synopsis" on the tool details page. Also the field "Name" is not showing the tool name or tool suite name - they are showing the tool or tool suite ID. I would suggest using three columns / text boxes: ID, Name, Description e.g. based on the current XML file for this tool of mine, ID: seq_filter_by_id Name: Filter sequences by ID Description: from a tabular file I have previously commented on the problem with showing the "description" on its own without the context of the tool name as displayed in Galaxy: http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-June/005640.html and: http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004012.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004017.html http://lists.bx.psu.edu/pipermail/galaxy-dev/2010-December/004019.html One idea would be to show just the name in the left hand pane of Galaxy, with the description as a tool tip AND show this at the top of the tool main page in the central panel. This would encourage tool authors to write this field as a self contained synopsis, and make the left hand panel less text heavy. Peter

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missing link 'display at UCSC'
by colin molter 06 Jul '11

06 Jul '11

Hello all, sorry for the very basic question (I tried to find some answer on the mailing list or faq but without any success). So here is my problem: i installed a fresh copy of galaxy in my server with apache. everything looks fine (i managed to perform several analyses so far). The problem is that there is *no link to UCSC*!! For my BAM file, i just have: display at Ensembl Current<http://ampere.ulb.ac.be/galaxy/display_application/6505e875ddb66fd2/ensembl…> And for the pileup: view in GeneTrack<http://ampere.ulb.ac.be/galaxy/display_application/6505e875ddb66fd2/genetra…> display at Ensembl Current<http://ampere.ulb.ac.be/galaxy/display_application/6505e875ddb66fd2/ensembl…> any idea bout how to have this link back. thks again colin -- Colin Molter University of Brussels - InSilico Team - http://insilico.ulb.ac.be/

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