[galaxy-user] after 'trim sequences', 'map w/Bowtie' job has been waiting for days to run
Greetings, I am using Galaxy Main; On 8/1/2013, and after 'trimming sequences' on my 'FASTQ groomed' data, I attempted to align my (single-end) 'trimmed sequences' output data to 'hg19 Canonical male' with 'Map with Bowtie for Illumina' It is now 8/3/2013, and the 'Map with Bowtie for Illumina' job has been 'waiting to run' +48hrs. I have 're-newed' the history several times, but have not deleted or re-run the original job for fear of losing my place in the queue. To check if 'canonical male' was the problem, I queued a second alignment to be 'mapped w/bowtie for Illumina' against hg19 (no sex); this job has also not run after being queued mor than 24 hours ago. Can you tell me if the delay is because I've done something incorrectly or if there's some action I can take to speed things? your help is deeply and sincerely appreciated https://main.g2.bx.psu.edu/u/theresa-stueve/h/1stunsupctcfupload-1 -- (Theresa) Ryan Stueve Department of Preventive Medicine Ite Laird-Offringa Lab NTT 6420 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Egg build failed for numpy 1.6.0
Hi, I am preferentially using the main server. But recently I have also tried to build a local Galaxy server. I also have a mac (Mac Pro OSx 10.6.8). Since I am not a specialist at all, I asked some kind of expert people from my institute. They told me that installing Galaxy on Mac can really be nightmare because there are some conflicts in the versions of python... This could explain the problem you are encountering with the egg dependencies. So they advised me to install an Ubuntu (12.04) operating system in a virtual machine using Virtual box. This is supposed to be much easier to install Galaxy and indeed, the installation of my local galaxy server ran fast and well. However, I don't know whether the tip is good or not, because I am now facing big problems with the virtual machine: the Ubuntu virtual machine is very unstable and often crashes while running big datas on Galaxy... The problem does not come from Galaxy, but from either Ubuntu guest system, the virtual machine or the communication with the mac host system and I haven't found out how to fix it yet. But since your version of Mac is different, you can try this solution, it might work better in your configuration. Hope that helps, Fabrice But at the moment, I have lots of problem with the Hi, I am trying to install a local version of galaxy on my mac book (x86_64, OSx 10.8.4). I seem to be having a lot of trouble with fetching and installing specific egg dependencies. Initially pysam was giving me trouble, but once I ran scramble.py -e pysam, the problem was fixed. Now I have trouble with the numpy egg dependency. Does anyone have any idea why a egg would fail to build. I am assuming it is because I have a more recent numpy version (1.7.1) installed already. What should I do, short of uninstalling the newer version of numpy ? Any help on the matter would be greatly appreciated. Thank you. L -- === Dr. Lahcen Campbell Contact: lahcencampb...@gmail.com http://bioinf.may.ie/index.html === ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Fabrice Besnard Institute of Biology of the Ecole Normale Supérieure (IBENS) 46 rue d'Ulm, 75230 Paris cedex 05, France 8th floor. Office: Room 802. Lab: Room 817. mail: fbesn...@biologie.ens.fr Tel: +33-1-44-32-39-44 ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] 2014 Galaxy Training Survey
Hello all, The Galaxy Project is asking for your help on how we should focus our training efforts for the coming year. If you are interested in Galaxy Training, please take a few minutes to let us know what you would like to see offered, and where you would like training to be held: http://bit.ly/gxy14training Thanks in advance for your time and input, Dave C -- http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-user] Fwd: HCC Analysis Pipeline
Hi Moritz, I'm forwarding your message to galaxy-user mailing list and Jennifer from Galaxy. Between the two, you should be able to get some help because unfortunately this is not my area of expertise so I'm afraid I won't be of much help. Good luck, Enis -- Forwarded message -- From: Moritz Juchler juch...@stud.uni-heidelberg.de Date: Fri, Aug 2, 2013 at 6:52 PM Subject: Re: HCC Analysis Pipeline To: enis.af...@irb.hr Sorry Mr. Afgan, I messed up with the history. This is the current one: https://main.g2.bx.psu.edu/u/mj--/h/whole-exome-somatic-gene-mutation-extraction-1 Or you just ignore the older message, I included the message above: Dear Sir Afgan, I am Moritz Juchler from University Heidelberg. I read through your slides for Bioblend and noticed that maybe you could help me with my problem. For my Bachelor thesis I have to setup GalaxyProject to find SNP's in genomes from hcc patients. I have a server on which I installed Galaxy locally, since we have a) very large files (30GB per patient) and b) the data is protection sensitive. My goal is to do the first 5 steps of this pipeline: http://www.nature.com/ng/journal/v44/n6/extref/ng.2256-S1.pdf (page 2) from this paper: http://www.nature.com/ng/journal/v44/n6/pdf/ng.2256.pdf This is my current workflow: https://main.g2.bx.psu.edu/u/mj--/w/workflow-whole-exome-somatic-gene-mutation-extraction and the matching *executed* history (with results) https://main.g2.bx.psu.edu/u/mj--/h/whole-exome-somatic-gene-mutation-extraction-1 My question is: Am I going in the right direction? I really dont know if I'm doing the correct steps :( Are there any links or papers that explain which specific tool I have to use for the first five steps? Of course if you do not have the time to answer my question, please refer me to someone who can answer the question and maybe has the time for it. Best Moritz On 2 August 2013 18:50, Moritz Juchler juch...@stud.uni-heidelberg.dewrote: Dear Sir Afgan, I am Moritz Juchler from University Heidelberg. I read through your slides for Bioblend and noticed that maybe you could help me with my problem. For my Bachelor thesis I have to setup GalaxyProject to find SNP's in genomes from hcc patients. I have a server on which I installed Galaxy locally, since we have a) very large files (30GB per patient) and b) the data is protection sensitive. My goal is to do the first 5 steps of this pipeline: http://www.nature.com/ng/journal/v44/n6/extref/ng.2256-S1.pdf (page 2) from this paper: http://www.nature.com/ng/journal/v44/n6/pdf/ng.2256.pdf This is my current workflow: https://main.g2.bx.psu.edu/u/mj--/w/workflow-whole-exome-somatic-gene-mutation-extraction and the matching *executed* history (with results) https://main.g2.bx.psu.edu/u/mj--/h/clean-whole-exome-somatic-gene-mutation-extraction-active-items-only My question is: Am I going in the right direction? I really dont know if I'm doing the correct steps :( Are there any links or papers that explain which specific tool I have to use for the first five steps? Of course if you do not have the time to answer my question, please refer me to someone who can answer the question and maybe has the time for it. Best Moritz ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Fwd: HCC Mutations Workflow on Local Galaxy Instance
Hi Moritz, For a quick breakdown of a variant pipeline, this recent workshop has slides. Basically you map (BWA is a good choice), choose a variant caller (Freebayes or other), and look at associated annotation ( SnpEff): http://wiki.galaxyproject.org/Events/GCC2013/TrainingDay#Variant_and_SNP_Analysis_with_Galaxy Tools in the group NGS: QC and manipulation such as FastQC should be able to help with quality checks and then others in same group with manipulations. For the detailed steps of sorting out known SNPs, synomymous vs non-synonymous, etc, you have a few choices. The tools in the groups ' NGS: GATK Tools (beta)', ' Phenotype Association', and 'Genome Diversity' are the places to look. Tools have help on the forms, including links to publications. Or you can look in the tool shed for more choices to use in your local instance: http://toolshed.g2.bx.psu.edu/ If the data in the shared link is really patient data that is protection sensitive, I would recommend unsharing the history and deleting the data permanently from the public Main Galaxy instance. Good luck with your thesis! Jen Galaxy team On 7/23/13 2:22 AM, Moritz Juchler wrote: Hello Ladies and Gentlemen, I am Moritz Juchler from University Heidelberg. For my Bachelor thesis I have to setup Galaxy to find SNP's in genomes from hcc patients. I have a 64-bit openSuse 11.3 server on which I installed Galaxy locally, since we have a) very large files (30GB per patient) and b) the data is protection sensitive. I have to run this pipeline: http://www.nature.com/ng/journal/v44/n6/extref/ng.2256-S1.pdf (page 2) from this paper: http://www.nature.com/ng/journal/v44/n6/pdf/ng.2256.pdf I have in fact some data from exactly these patients, and I want to reproduce the pipeline as similar as possible. I have this so far: https://main.g2.bx.psu.edu/u/mj--/w/ngs I would be glad to even do 2-3 steps, I wont need much more for my thesis. But I find it so hard to find any information about what to do in Galaxy in practice. The first step in the workflow of the paper I included are the statistics on page 1 of the supplements, but those aren't necessary (?). So the first step I have to do after the alignment and the sam to bam conversion and the dedupe is the first step on page 2 of the supplements: Variant calling Tumor Which tool in Galaxy do I have to use in order to do this and the following steps? Any hints, links to papers or answers are welcome :) Best Moritz ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Rename tool output file in Galaxy
Hello Sachit, If you are running a local Galaxy, the full path to datasets is noted on the "info" page, found by clicking on the circled "i" icon between the disc and blue re-run button. You can click on the pencil icon (top upper right corner) and rename the user labels any time you want, unless the file is being processed. In that case, wait until it is done, then change. Changing the Galaxy internal name of the file is not recommended, but is probably possible. However, expect the unexpected if you attempt this, as the changes would not be easy for us to support. To let you know, you may find the the galaxy-...@bx.psu.edu mailing list better for technical local Galaxy questions going forward. Take care, Jen Galaxy team On 7/23/13 7:13 AM, Sachit Adhikari wrote: Hi group, The galaxy stores the output of the job on files/043/dataset_ID.dat. I have two questions here.: 1) Can I find the ID of my output from the Galaxy history? I tried Edit Attributes, Annotations, tags but couldn't find it. 2) Can I rename my output while initiating the task? If I can how can I do this and what are the consequences. Thank you. Regards, Sachit ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] Galaxy server down?
I am also dead in the water. I sent a post to this effect last week. Last Friday I left a job queued up on the main server and as of this morning, it still had not run after 2-1/2 days. Can someone notify us about what is wrong, and what is being done to fix it? Best regards, Sam From: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] on behalf of Anto Praveen Rajkumar Rajamani [a...@hum-gen.au.dk] Sent: Monday, August 05, 2013 7:53 AM To: Elizabeth Clare; galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Galaxy server down? Hello, I am on the same boat. I experience similar problems. What is wrong with Galaxy? Best wishes, Anto From: galaxy-user-boun...@lists.bx.psu.edu [galaxy-user-boun...@lists.bx.psu.edu] on behalf of Elizabeth Clare [elclare.evol.biol...@gmail.com] Sent: 04 August 2013 11:04 To: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Galaxy server down? Hi, I think Galaxy was down earlier this week - I saw several several messages when trying to access the public server, but I'm still getting no function on the public site. Are there still problems? I can load the page now, make new workflows and set tasks but no tasks have been completed in a few days. For example, I set a file to upload yesterday and it still has the blue working indication. Tasks from two days ago are grey and waiting to run. Any ideas what has gone wrong? Beth On Fri, Aug 2, 2013 at 12:18 PM, Elizabeth Clare elclare.evol.biol...@gmail.commailto:elclare.evol.biol...@gmail.com wrote: Hi Jen, I have had little response from the galaxy public server in the last two days (I'm in England) (https://main.g2.bx.psu.edu). At the moment I cannot load the webpage or any page associated with it. I have had messages Internal Server Error then one about a brief shut down saying we should contact an administrator if it went on for a while. It appeared to come back early this morning but now is unresponsive again. I guess I'm reporting a continual error now. Has it gone down? Thanks, Beth -- Dr. Elizabeth L. Clare School of Biological and Chemical Sciences Queen Mary University of London Mile End Road, London E1 4NS Room 1.02, G. E. Fogg Building e.cl...@qmul.ac.ukmailto:e.cl...@qmul.ac.uk +44 (0)207 882 5687tel:%2B44%20%280%29207%20882%205687 http://webspace.qmul.ac.uk/eclare/ If you say yes more often than you say no, you will do interesting things in your life -- Dr. Elizabeth L. Clare School of Biological and Chemical Sciences Queen Mary University of London Mile End Road, London E1 4NS Room 1.02, G. E. Fogg Building e.cl...@qmul.ac.ukmailto:e.cl...@qmul.ac.uk +44 (0)207 882 5687 http://webspace.qmul.ac.uk/eclare/ If you say yes more often than you say no, you will do interesting things in your life ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-user] question
Hello Larry,
The Manipulate Fastq tool only brings up the regular trimmer tools
again once sequence and trim are selected, so this will not work. And
a regular expression could be used as a filter, but that will not
actually trim the data.
If you choose to filter, this regular expression would find sequences
with variable length poly-G at the end. This one actually finds one or
more, so not really poly - this is for you to modify. Change the number
in the {} to make a minimum required length.
^.*[A|T|C|N]G{1}G*$
Are you trying to trim poly-A? If using a local instance, repeat masker
was just added to the Tool Shed and could be quicker. But if using the
public Main server, the adapter clip idea from Ido is very good -
certainly worth a try.
The other option is to just go ahead and align the data. If the region
is long for all sequences, or some subset (you could pull out those that
are very long), then do a blanket end length trim on all, put back
together any files you have split apart, and let the aligner deal with
the remaining trailing bases. Manipulate Fastq can be used to subset
the file - just run it twice (or as many times as needed to get all the
data uniquely into distinct files to merge later.
Best,
Jen
Galaxy team
On 7/28/13 11:44 AM, Larry Simpson wrote:
Hi
Is it possible to trim a variable number of a specific nucleotide from
the 3' ends of fastq RNA reads? The Manipulate Fastq utility in
Galaxy may have this ability but I do not know how to create a custom
inquiry.
Thanks in advance for any assistance.
Larry
___
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:
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To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
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--
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org
___
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/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
[galaxy-user] Galaxy Log-In and DATA
Hi... I haven't used Galaxy for a while, and forgot my password. The problem with resetting it is that the email I used is no longer active: I graduated. I need to access the files I uploaded, as its appearing that they did not collapse in the 'collapse' function properly: I have the same region of a reference genome mapping to multiple sequences with 100% ID. Can I please get access to the account? My previous email was: mer...@uta.edu Thank you! Mersee -- M.J. Madison-Villar, PhD Postdoctoral Fellow, Colorado State University ___ 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/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
