Re: [galaxy-dev] Anyone has tools for NCBI Lite-SRA format ?
Hi, We are getting multiple requests for this but did not have the bandwidth to do it. So if you are planning to implement - share through the toolshed and we will roll it to main. The way I got round this was let the SRA website do the conversion. So just paste in the URL in the upload screen: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=dloadrun_list=SRRXXformat=fastq Where SRRXX is the archive of interest, and it downloads Sanger FASTQ sequences to Galaxy. Regards, Steve ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Updating BLAST+ wrapper
On Mon, Apr 4, 2011 at 12:19 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Fri, Apr 1, 2011 at 12:01 PM, Peter Cock p.j.a.c...@googlemail.com wrote: On Thu, Mar 31, 2011 at 6:28 PM, Peter Cock p.j.a.c...@googlemail.com wrote: Hi all, The NCBI have just released BLAST 2.2.25+ which includes some interesting new stuff of interest to the tabular output, ... One reason why I want to move to BLAST 2.2.25+ on our local machine is they fixed the subject IDs in tabular output, ... Hi Kanwei, Could you transplant or merge this commit please? https://bitbucket.org/peterjc/galaxy-central/changeset/ab40f95393ec It updates the test output files to work with BLAST 2.2.25+, which I will be using locally due to several important bug fixes. As you don't offer BLAST+ on the Penn State server I don't expect this to cause you any problems. Also (and unrelated to this change), do you see this from the test suite? $ ./run_functional_tests.sh -id ncbi_blastp_wrapper ... == ERROR: NCBI BLAST+ blastp ( ncbi_blastp_wrapper ) Test-1 -- Traceback (most recent call last): File /home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py, line 155, in test_tool self.do_it( td ) File /home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py, line 71, in do_it page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[0], all_inputs) File /home/pjcock/repositories/galaxy-central/test/functional/test_toolbox.py, line 122, in __expand_grouping elif isinstance(declared_inputs[value.name], str): KeyError: 'blast_type' Solved, it seems I can't omit any parameters in the test and expect the defaults to be used. This doesn't seem desirable (new bug?), but the quick fix is to add a few lines to the test. Could you commit this too: https://bitbucket.org/peterjc/galaxy-central/changeset/124e4556f3c5 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Updating BLAST+ wrapper
On Mon, Apr 4, 2011 at 4:03 PM, Kanwei Li kan...@gmail.com wrote: I tried both ways, no dice (you can try yourself with a clean galaxy-central base) I'm a bit puzzled and not an hg expert. Was there an error message? And for plan (B), what went wrong with using patch and the raw changes? Surely that should work? https://bitbucket.org/peterjc/galaxy-central/changeset/ab40f95393ec/raw/galaxy-central-ab40f95393ec.diff https://bitbucket.org/peterjc/galaxy-central/changeset/124e4556f3c5/raw/galaxy-central-124e4556f3c5.diff 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Password input field for tools?
Hi Daniel, I have attached a patch that does this below. You can use it by setting param type=password However the security is lacking as you can see the string when you try to re-run the job and view source. Is this sufficient for your purposes? Thanks, K On Sat, Apr 2, 2011 at 11:01 AM, Daniel Schmidt danielschmid...@gmx.net wrote: Hi all! Is there any way to use password input fields (input type=password...) with tools? A tools XML definition file only seems to support text and textarea fields. I already tried setting a tools parameter type to password, which unfortunately results in an Unknown tool parameter type 'password'. Trying password=True (like area=True) does not result in an error, but the text field is still just a normal text field. I may be mistaken, as I am new to Python and Galaxy, but there already seems to be a PasswordField class and a TextField class, which both can be found in several files. Was the PasswordField class for tool parameters maybe disabled for a reason? Thanks! Daniel ___ 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: http://lists.bx.psu.edu/ passwordparam.patch Description: Binary data ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Freebayes
This fix got me further, however I'm now getting the following error, which is now more confusing... [bam_sort_core] merging from 40 files... BGZF ERROR: unable to open file 1.0 BGZF ERROR: unable to open file 1.0 Could not open input BAM files Juan On Apr 1, 2011, at 1:53 PM, Dannon Baker wrote: Juan, What version of freebayes are you running? The freebayes configuration in the galaxy repository was written with the .4 series in mind, and it appears that the options have changed with the .6 series. We'll update the tool config, but in the meanwhile you could probably get it working again for your local use by editing the tools/human_genome_variation/freebayes.xml file to comment out the no-longer-valid parameter in line 34: -Y $params.postIntegBanddepth Let me know if this doesn't get things moving again for you, Dannon On Apr 1, 2011, at 1:17 PM, Juan Carlos Perin wrote: I'm trying to run Freebayes SNP calling on a bam file from a BWA alignment of solid data. I keep getting the following error: [bam_sort_core] merging from 40 files... freebayes: invalid option -- Y did you mean --bam ? I'm not sure where this is set in the code to try to debug things. I'm wondering if anyones had this error, and how to fix it? Just to note, I'm running Brad Chapmans branch of galaxy for the LIMS functionality. But it appears to be an issue with either galaxy-dist or this one. Thanks in advance for any advice. Juan Perin ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] how to purge histories/datasets not accessed/updated for a certain time
Hi, We have a local mirror of the galaxy system and the disk is occupied really quickly. Is there a way to purge histories/datasets not accessed/updated for a certain period of time, no matter if they are deleted by the user? It looks like the current scripts for clean up only purges deleted histories/datasets. Thanks! Chaolin ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Updating BLAST+ wrapper
On Mon, Apr 4, 2011 at 4:36 PM, Kanwei Li kan...@gmail.com wrote: dhcp243253:galaxy-central kanwei$ hg transplant -s ~/peter/galaxy-central/ -b blast25 searching for changes changeset: 5585:ab40f95393ec branch: blast25 parent: 5583:086c9c2c52b9 user: peterjc p.j.a.c...@googlemail.com date: Mon Apr 04 12:12:11 2011 +0100 summary: Update tests for NCBI BLAST 2.2.25+ which fixed subject ID in tabular output apply changeset? [ynmpcq?]: y changeset: 5586:124e4556f3c5 branch: blast25 user: peterjc p.j.a.c...@googlemail.com date: Mon Apr 04 14:44:52 2011 +0100 summary: Include optional parameters in BLASTP test to avoid KeyError apply changeset? [ynmpcq?]: y searching for changes adding changesets adding manifests adding file changes added 2 changesets with 4 changes to 4 files dhcp243253:galaxy-central kanwei$ hg tip changeset: 5338:124e4556f3c5 branch: blast25 tag: tip user: peterjc p.j.a.c...@googlemail.com date: Mon Apr 04 14:44:52 2011 +0100 summary: Include optional parameters in BLASTP test to avoid KeyError The above is strange - why have you got a blast25 branch? Maybe the transplant isn't working as expected... dhcp243253:galaxy-central kanwei$ hg push pushing to https://kan...@bitbucket.org/galaxy/galaxy-central/ searching for changes abort: push creates new remote branches: blast25! (use 'hg push --new-branch' to create new remote branches) dhcp243253:galaxy-central kanwei$ hg merge blast25 abort: merging with a working directory ancestor has no effect It looks like you are on the blast25 branch, try checking out default then merging the new blast25 branch. It should be a fast-forward merge (just the two commits). Then you can push default back to galaxy-central on bitbucket. I think. Importing the diffs gives merge error Are you using a hg command here? What I meant for the Plan B was just using the Unix command patch to apply my changes by hand to the default branch. Then commit it under your name. It won't be associated with my bitbucket account, but it should just work. 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Updating BLAST+ wrapper
Done the manual way ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Password input field for tools?
Daniel, Note that this (and similar) password solutions in Galaxy is not secure in any real way (especially if you're dealing with patient data or HIPPA): The password (hidden or visible in a text field) is still transmitted in clear-text over the network (unless you're using HTTPS/SSL). If your users are connecting over WiFi (and the wireless network is not encrypted) - it's very easy to find the password. The password will also be saved in clear-text in the Galaxy database, and will be saved in the galaxy log files (as it will be passed to the program on the command line). Of course, depending on your configuration and requirements, this solution might suffice, but be aware that it provides a false sense of security, basically protecting only against people standing behind the user's back and looking at his monitor. Just my two cents, -gordon Kanwei Li wrote, On 04/04/2011 12:34 PM: Well, it could be modified to never return a value back to the interface after being set. Would that be sufficient? On Mon, Apr 4, 2011 at 11:46 AM, Daniel Schmidt danielschmid...@gmx.net wrote: Hello all! Thanks alot K! Although I have to admit, that it seems too insecure, at least for the tool I am currently working on. The password field is needed to connect to a database, which contains (sensitive) patient data. Revealing the password to someone else by accident when re-running a job could give him or her access to data he or she should have never access to. In spite of everything, thank you again! Daniel Am 04.04.2011 17:17, schrieb Kanwei Li: Hi Daniel, I have attached a patch that does this below. You can use it by settingparam type=password However the security is lacking as you can see the string when you try to re-run the job and view source. Is this sufficient for your purposes? Thanks, K On Sat, Apr 2, 2011 at 11:01 AM, Daniel Schmidtdanielschmid...@gmx.net wrote: Hi all! Is there any way to use password input fields (input type=password...) with tools? A tools XML definition file only seems to support text and textarea fields. I already tried setting a tools parameter type to password, which unfortunately results in an Unknown tool parameter type 'password'. Trying password=True (like area=True) does not result in an error, but the text field is still just a normal text field. I may be mistaken, as I am new to Python and Galaxy, but there already seems to be a PasswordField class and a TextField class, which both can be found in several files. Was the PasswordField class for tool parameters maybe disabled for a reason? Thanks! Daniel ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/ ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] Alternative Bowtie/TopHat tools
More bug fixes, and a paired-end TopHat tool. Available here: http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_2011_04_04.tar.bz2 See the interface here: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_pe1 Comments are very welcomed, Cufflinks is next, -gordon Assaf Gordon wrote, On 03/30/2011 09:21 AM: Still very much work-in-progress, but I'd like to hear any comments or ideas that you might have. No need to install, just visit here to see TopHat's interface: http://cancan.cshl.edu/publicgalaxy/root?tool_id=cshl_tophat_se1 Main differences from the existing TopHat tool: 1. Far fewer visible options 2. Select Existing gene mode (use GTF file) or do De-novo junction detection (or both) 3. Allow insertions/deletions detection (with the latest tophat). 4. Allow user to specify custom command line parameters. 5. Accepts Fasta, FastqSanger, FastqIllumina (but not generic fastq, per your feedback). If you think there are other critical and often used options, let me know. updated code is available here: http://cancan.cshl.edu/labmembers/gordon/files/cshl_rnaseq_tools_1.tar.bz2 -gordon ___ 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: http://lists.bx.psu.edu/
