Re: [galaxy-dev] [galaxy-user] Why SGE needed for galaxy ?
Thanks Enis, The paper is good , i was looking something like it. Ok, I will use CBL , just a small query : we use CBL for cloud man purpose, i think yes . Should we use the same Image for workers and enable cloudman script to use that one for launching nodes ? BR Zeeshan On W7-Feb 11, 2013, at 9:27 PM, Enis Afgan wrote: Here's a link to the architecture paper: http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full Building CloudMan image from the repo you mention will not work - that repo is for cloudman itself while you need an image capable of running cloudman. For that, you should use CBL. Also, here are some instructions about setting up cloudman and galaxy on OpenNebula cloud: https://www.cloud.sara.nl/projects/mattiasdehollander-project/wiki (note that this mentions use of mi-deployment set of scripts; since that, mi-deployment has been merged into CBL). On Mon, Feb 11, 2013 at 8:21 PM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Hi, Thanks for answers , Actually i tried to understand cloudman role in galaxy , do you have an architecture paper which i should read ? for e.g. what i unserstood si that cloud man runs a python server and manage SGE through it via some python script . (may be i am wrong) Our proposed installation is like this: Users launch cloud man from Open nebula cloud, when cloudman is running they can add more nodes which are endup in same private cloud. As you suggested in this particular case I should have same images both for (master cloudman) and workers , am i right ? actually i built one image via https://bitbucket.org/galaxy/cloudman . DO you suggest that I should built image from CBL tree you mentioned below ? which wd have both cloudman and galaxy together. BR Zeeshan On W6-Feb 8, 2013, at 10:21 PM, Enis Afgan wrote: As far as actually building the image, the recommended method is to use CloudBioLinux build scripts: https://github.com/chapmanb/cloudbiolinux There is a CloudMan flavor of CBL that allows you to build only CloudMan- and Galaxy-required parts: https://github.com/chapmanb/cloudbiolinux/tree/master/contrib/flavor/cloudman On Sat, Feb 9, 2013 at 12:24 AM, Dannon Baker dannonba...@me.com wrote: The workers don't need their own copy of galaxy installed, but a shared filesystem is a requirement for galaxy (in any cluster environment -- see the galaxy wiki for more http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster). Cloudman handles managing NFS for you and sharing the galaxy/tools/index/data volumes. In order for workers to communicate with the master instance, they'll need the cloudman installation as well, so you should use the same image. Now that I've answered that, I'm not sure I totally understand your proposed installation yet, but if you're suggesting bypassing cloudman for installation on a private cloud it should be possible. You'd want the master instance up full time running as the galaxy front end, dispatching jobs to a separate cluster managed by SGE/PBS/whatever. Basically the standard cluster configuration outlined in the wiki above, but you'd want your worker nodes automatically configured to mount the shared directories and join the PBS/SGE queue so they could handle jobs. Depending on what type of private cloud you're working with, it might be easier to just see if you can get cloudman to work :) Lastly, I swapped this message to galaxy-dev since it's about installation nuts and bolts. -Dannon On Feb 8, 2013, at 3:02 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Dear Enis, thanks for reply and being you as cloudman developer it is good to see you in the list . Q2: On Workers node we need galaxy installed with its shared directories ? like galaxyindices , galaxydata Q3: For a private cloud setup do you prefare to have a master image with cloudman and galaxy and use the same image for workers as well ? or worker images can be vanilla OS ? BR Zeeshan On W6-Feb 7, 2013, at 11:50 PM, Enis Afgan wrote: Hi Zeeshan, In order to gain from the scalability of the cloud, SGE does need to run. However, CloudMan sets all that up and manages it going forward. Enis On Fri, Feb 8, 2013 at 8:59 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Hi, It seems that cloud man need SGE for scaling . Does SGE need also when run cloud on private cloud ? Zeeshan ___ 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-dev] Bug in Galaxy Reports tool
Hi all, Running ~/galaxy-dist/run_reports.sh brings up the Galaxy Reports interface on poort 9001. When clicking on 'Jobs per user' - picking a user - picking a month - and clicking on 'State' in the bar at the top, clears the screen. Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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] [galaxy-user] Why SGE needed for galaxy ?
Yes, you use the same image for both masters and the workers. -Dannon On Feb 12, 2013, at 5:46 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Thanks Enis, The paper is good , i was looking something like it. Ok, I will use CBL , just a small query : we use CBL for cloud man purpose, i think yes . Should we use the same Image for workers and enable cloudman script to use that one for launching nodes ? BR Zeeshan On W7-Feb 11, 2013, at 9:27 PM, Enis Afgan wrote: Here's a link to the architecture paper: http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full Building CloudMan image from the repo you mention will not work - that repo is for cloudman itself while you need an image capable of running cloudman. For that, you should use CBL. Also, here are some instructions about setting up cloudman and galaxy on OpenNebula cloud: https://www.cloud.sara.nl/projects/mattiasdehollander-project/wiki (note that this mentions use of mi-deployment set of scripts; since that, mi-deployment has been merged into CBL). On Mon, Feb 11, 2013 at 8:21 PM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Hi, Thanks for answers , Actually i tried to understand cloudman role in galaxy , do you have an architecture paper which i should read ? for e.g. what i unserstood si that cloud man runs a python server and manage SGE through it via some python script . (may be i am wrong) Our proposed installation is like this: Users launch cloud man from Open nebula cloud, when cloudman is running they can add more nodes which are endup in same private cloud. As you suggested in this particular case I should have same images both for (master cloudman) and workers , am i right ? actually i built one image via https://bitbucket.org/galaxy/cloudman . DO you suggest that I should built image from CBL tree you mentioned below ? which wd have both cloudman and galaxy together. BR Zeeshan On W6-Feb 8, 2013, at 10:21 PM, Enis Afgan wrote: As far as actually building the image, the recommended method is to use CloudBioLinux build scripts: https://github.com/chapmanb/cloudbiolinux There is a CloudMan flavor of CBL that allows you to build only CloudMan- and Galaxy-required parts: https://github.com/chapmanb/cloudbiolinux/tree/master/contrib/flavor/cloudman On Sat, Feb 9, 2013 at 12:24 AM, Dannon Baker dannonba...@me.com wrote: The workers don't need their own copy of galaxy installed, but a shared filesystem is a requirement for galaxy (in any cluster environment -- see the galaxy wiki for more http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster). Cloudman handles managing NFS for you and sharing the galaxy/tools/index/data volumes. In order for workers to communicate with the master instance, they'll need the cloudman installation as well, so you should use the same image. Now that I've answered that, I'm not sure I totally understand your proposed installation yet, but if you're suggesting bypassing cloudman for installation on a private cloud it should be possible. You'd want the master instance up full time running as the galaxy front end, dispatching jobs to a separate cluster managed by SGE/PBS/whatever. Basically the standard cluster configuration outlined in the wiki above, but you'd want your worker nodes automatically configured to mount the shared directories and join the PBS/SGE queue so they could handle jobs. Depending on what type of private cloud you're working with, it might be easier to just see if you can get cloudman to work :) Lastly, I swapped this message to galaxy-dev since it's about installation nuts and bolts. -Dannon On Feb 8, 2013, at 3:02 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Dear Enis, thanks for reply and being you as cloudman developer it is good to see you in the list . Q2: On Workers node we need galaxy installed with its shared directories ? like galaxyindices , galaxydata Q3: For a private cloud setup do you prefare to have a master image with cloudman and galaxy and use the same image for workers as well ? or worker images can be vanilla OS ? BR Zeeshan On W6-Feb 7, 2013, at 11:50 PM, Enis Afgan wrote: Hi Zeeshan, In order to gain from the scalability of the cloud, SGE does need to run. However, CloudMan sets all that up and manages it going forward. Enis On Fri, Feb 8, 2013 at 8:59 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Hi, It seems that cloud man need SGE for scaling . Does SGE need also when run cloud on private cloud ? Zeeshan ___ 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
Re: [galaxy-dev] Bug in Galaxy Reports tool
Hello joachim, Thanks for reporting this. I've added a Trello card for this issue: https://trello.com/card/galaxy-reports/506338ce32ae458f6d15e4b3/610 Greg Von Kuster On Feb 12, 2013, at 6:05 AM, Joachim Jacob |VIB| wrote: Hi all, Running ~/galaxy-dist/run_reports.sh brings up the Galaxy Reports interface on poort 9001. When clicking on 'Jobs per user' - picking a user - picking a month - and clicking on 'State' in the bar at the top, clears the screen. Thanks, Joachim -- Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib ___ 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] [galaxy-user] Why SGE needed for galaxy ?
Thanks Dannon. BR Zeeshan On W7-Feb 12, 2013, at 12:22 PM, Dannon Baker wrote: Yes, you use the same image for both masters and the workers. -Dannon On Feb 12, 2013, at 5:46 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Thanks Enis, The paper is good , i was looking something like it. Ok, I will use CBL , just a small query : we use CBL for cloud man purpose, i think yes . Should we use the same Image for workers and enable cloudman script to use that one for launching nodes ? BR Zeeshan On W7-Feb 11, 2013, at 9:27 PM, Enis Afgan wrote: Here's a link to the architecture paper: http://onlinelibrary.wiley.com/doi/10.1002/cpe.1836/full Building CloudMan image from the repo you mention will not work - that repo is for cloudman itself while you need an image capable of running cloudman. For that, you should use CBL. Also, here are some instructions about setting up cloudman and galaxy on OpenNebula cloud: https://www.cloud.sara.nl/projects/mattiasdehollander-project/wiki (note that this mentions use of mi-deployment set of scripts; since that, mi-deployment has been merged into CBL). On Mon, Feb 11, 2013 at 8:21 PM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Hi, Thanks for answers , Actually i tried to understand cloudman role in galaxy , do you have an architecture paper which i should read ? for e.g. what i unserstood si that cloud man runs a python server and manage SGE through it via some python script . (may be i am wrong) Our proposed installation is like this: Users launch cloud man from Open nebula cloud, when cloudman is running they can add more nodes which are endup in same private cloud. As you suggested in this particular case I should have same images both for (master cloudman) and workers , am i right ? actually i built one image via https://bitbucket.org/galaxy/cloudman . DO you suggest that I should built image from CBL tree you mentioned below ? which wd have both cloudman and galaxy together. BR Zeeshan On W6-Feb 8, 2013, at 10:21 PM, Enis Afgan wrote: As far as actually building the image, the recommended method is to use CloudBioLinux build scripts: https://github.com/chapmanb/cloudbiolinux There is a CloudMan flavor of CBL that allows you to build only CloudMan- and Galaxy-required parts: https://github.com/chapmanb/cloudbiolinux/tree/master/contrib/flavor/cloudman On Sat, Feb 9, 2013 at 12:24 AM, Dannon Baker dannonba...@me.com wrote: The workers don't need their own copy of galaxy installed, but a shared filesystem is a requirement for galaxy (in any cluster environment -- see the galaxy wiki for more http://wiki.galaxyproject.org/Admin/Config/Performance/Cluster). Cloudman handles managing NFS for you and sharing the galaxy/tools/index/data volumes. In order for workers to communicate with the master instance, they'll need the cloudman installation as well, so you should use the same image. Now that I've answered that, I'm not sure I totally understand your proposed installation yet, but if you're suggesting bypassing cloudman for installation on a private cloud it should be possible. You'd want the master instance up full time running as the galaxy front end, dispatching jobs to a separate cluster managed by SGE/PBS/whatever. Basically the standard cluster configuration outlined in the wiki above, but you'd want your worker nodes automatically configured to mount the shared directories and join the PBS/SGE queue so they could handle jobs. Depending on what type of private cloud you're working with, it might be easier to just see if you can get cloudman to work :) Lastly, I swapped this message to galaxy-dev since it's about installation nuts and bolts. -Dannon On Feb 8, 2013, at 3:02 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Dear Enis, thanks for reply and being you as cloudman developer it is good to see you in the list . Q2: On Workers node we need galaxy installed with its shared directories ? like galaxyindices , galaxydata Q3: For a private cloud setup do you prefare to have a master image with cloudman and galaxy and use the same image for workers as well ? or worker images can be vanilla OS ? BR Zeeshan On W6-Feb 7, 2013, at 11:50 PM, Enis Afgan wrote: Hi Zeeshan, In order to gain from the scalability of the cloud, SGE does need to run. However, CloudMan sets all that up and manages it going forward. Enis On Fri, Feb 8, 2013 at 8:59 AM, Zeeshan Ali Shah zas...@pdc.kth.se wrote: Hi, It seems that cloud man need SGE for scaling . Does SGE need also when run cloud on private cloud ? Zeeshan ___ 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
[galaxy-dev] Preffered way of running a tool on multiple input files
Hi, I'm looking for a preferred way of running Bowtie (or any other tool) on multiple input files and run statistics on the Bowtie output afterwards. The input is a directory of files fastq1..fastq100 The bowtie output should be bed1...bed100 The statistics tool should run on bed1...bed100 and return xls1..xls100 Then I will write a tool which will get xls1..xls100 and merge them to one final output. I searched for a smiliar cases, and I couldn't figure anyone which had this problem before. Can't use the parallelism tag, because what will be the input for each tool? it should be a fastq file not a directory of fastq files. Neither I would like to run each fastq file in a different workflow - creating a mess. I thought only on two solutions: 1. Implement new datatypes: bed_dir fastq_dir and implements new tool wrappers which will get a folder instead of a file. 2. merge the input files before sending to bowtie, and use parallelism tag to make them be splitted merged again on each tool. Does anyone has any better suggestion? Thanks, Hagai ___ 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] Preffered way of running a tool on multiple input files
Hi Hagai, Actually, using a workflow, you are able to select multiple input files, and let the workflow run separately on all input files. I would proceed by creating a data library for all your fastq files, which you can upload via FTP, or via a system directory. You can use a sample of your fastq files to create the steps in a history you want to perform, and extract a workflow out of it. Next, copy all fastq files from a data library in a new history, and run your workflow on the all input files. I hope this helps you further, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 02/12/2013 04:02 PM, Hagai Cohen wrote: Hi, I'm looking for a preferred way of running Bowtie (or any other tool) on multiple input files and run statistics on the Bowtie output afterwards. The input is a directory of files fastq1..fastq100 The bowtie output should be bed1...bed100 The statistics tool should run on bed1...bed100 and return xls1..xls100 Then I will write a tool which will get xls1..xls100 and merge them to one final output. I searched for a smiliar cases, and I couldn't figure anyone which had this problem before. Can't use the parallelism tag, because what will be the input for each tool? it should be a fastq file not a directory of fastq files. Neither I would like to run each fastq file in a different workflow - creating a mess. I thought only on two solutions: 1. Implement new datatypes: bed_dir fastq_dir and implements new tool wrappers which will get a folder instead of a file. 2. merge the input files before sending to bowtie, and use parallelism tag to make them be splitted merged again on each tool. Does anyone has any better suggestion? Thanks, Hagai ___ 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] Preffered way of running a tool on multiple input files
Thanks for your answer. I figured that there is an option to run a workflow on multiple files, but I can't merge the outputs afterwardsl. I would like the workflow to return one final output. But you gave me another idea. Can I somehow tell one workflow to run on other workflow output? If this can be done, I can run 100 different workflows with bowtie statistics, each working on one fastq file, than run another workflow which gets 100 xls inputs and merge them to one. On Tue, Feb 12, 2013 at 5:20 PM, Joachim Jacob |VIB| joachim.ja...@vib.bewrote: Hi Hagai, Actually, using a workflow, you are able to select multiple input files, and let the workflow run separately on all input files. I would proceed by creating a data library for all your fastq files, which you can upload via FTP, or via a system directory. You can use a sample of your fastq files to create the steps in a history you want to perform, and extract a workflow out of it. Next, copy all fastq files from a data library in a new history, and run your workflow on the all input files. I hope this helps you further, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 02/12/2013 04:02 PM, Hagai Cohen wrote: Hi, I'm looking for a preferred way of running Bowtie (or any other tool) on multiple input files and run statistics on the Bowtie output afterwards. The input is a directory of files fastq1..fastq100 The bowtie output should be bed1...bed100 The statistics tool should run on bed1...bed100 and return xls1..xls100 Then I will write a tool which will get xls1..xls100 and merge them to one final output. I searched for a smiliar cases, and I couldn't figure anyone which had this problem before. Can't use the parallelism tag, because what will be the input for each tool? it should be a fastq file not a directory of fastq files. Neither I would like to run each fastq file in a different workflow - creating a mess. I thought only on two solutions: 1. Implement new datatypes: bed_dir fastq_dir and implements new tool wrappers which will get a folder instead of a file. 2. merge the input files before sending to bowtie, and use parallelism tag to make them be splitted merged again on each tool. Does anyone has any better suggestion? Thanks, Hagai __**_ 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] Preffered way of running a tool on multiple input files
Hagai, Jorrit Boekel and I have implemented essentially literally what you described. https://bitbucket.org/galaxy/galaxy-central/pull-request/116/multiple-file-datasets-implementation Merge this in to your Galaxy tree https://bitbucket.org/jmchilton/galaxy-central-multifiles-feb2013. Switch use_composite_multfiles to true in universe_wsgi.ini. Then you automatically get a multiple file version of each of your datatypes (so m:fastq, m:xls, etc...). Tools that process a singleton version of a datatype can seamlessly process a multiple file version of that dataset in parallel and the outputs that are created as a result are going to be of the multifile type of the original types. These datasets can be created using the multifile upload tool, a directory on the FTP server, or via library imports via API. Input names are preserved like you described. Some huge caveats: - The Galaxy team has expressed reservations about this particular implementation so it will never be officially supported. - Its early days and this is very experimental (use at your own risk). - I am pretty sure it is not going to work with bed files, since there is special logic in Galaxy to deal with bed indices (I think we can work around it by declaring a concrete m:bed type and replicated that logic, its on the TODO list but happy to accept contributions :) ). More discussion of this can be found at these places: http://www.youtube.com/watch?v=DxJzEkOasu4 https://bitbucket.org/galaxy/galaxy-central/pull-request/116/multiple-file-datasets-implementation http://dev.list.galaxyproject.org/pass-more-information-on-a-dataset-merge-td4656455.html -John On Tue, Feb 12, 2013 at 9:02 AM, Hagai Cohen haga...@gmail.com wrote: Hi, I'm looking for a preferred way of running Bowtie (or any other tool) on multiple input files and run statistics on the Bowtie output afterwards. The input is a directory of files fastq1..fastq100 The bowtie output should be bed1...bed100 The statistics tool should run on bed1...bed100 and return xls1..xls100 Then I will write a tool which will get xls1..xls100 and merge them to one final output. I searched for a smiliar cases, and I couldn't figure anyone which had this problem before. Can't use the parallelism tag, because what will be the input for each tool? it should be a fastq file not a directory of fastq files. Neither I would like to run each fastq file in a different workflow - creating a mess. I thought only on two solutions: 1. Implement new datatypes: bed_dir fastq_dir and implements new tool wrappers which will get a folder instead of a file. 2. merge the input files before sending to bowtie, and use parallelism tag to make them be splitted merged again on each tool. Does anyone has any better suggestion? Thanks, Hagai ___ 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] Preffered way of running a tool on multiple input files
You cannot directly couple different workflows. But you could indeed copy all outputs of the different workflows into one history, and create a separate workflow with your tool to work on all those input files. Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 02/12/2013 04:31 PM, Hagai Cohen wrote: Thanks for your answer. I figured that there is an option to run a workflow on multiple files, but I can't merge the outputs afterwardsl. I would like the workflow to return one final output. But you gave me another idea. Can I somehow tell one workflow to run on other workflow output? If this can be done, I can run 100 different workflows with bowtie statistics, each working on one fastq file, than run another workflow which gets 100 xls inputs and merge them to one. On Tue, Feb 12, 2013 at 5:20 PM, Joachim Jacob |VIB| joachim.ja...@vib.be mailto:joachim.ja...@vib.be wrote: Hi Hagai, Actually, using a workflow, you are able to select multiple input files, and let the workflow run separately on all input files. I would proceed by creating a data library for all your fastq files, which you can upload via FTP, or via a system directory. You can use a sample of your fastq files to create the steps in a history you want to perform, and extract a workflow out of it. Next, copy all fastq files from a data library in a new history, and run your workflow on the all input files. I hope this helps you further, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 tel:%2B32%209%20244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 02/12/2013 04:02 PM, Hagai Cohen wrote: Hi, I'm looking for a preferred way of running Bowtie (or any other tool) on multiple input files and run statistics on the Bowtie output afterwards. The input is a directory of files fastq1..fastq100 The bowtie output should be bed1...bed100 The statistics tool should run on bed1...bed100 and return xls1..xls100 Then I will write a tool which will get xls1..xls100 and merge them to one final output. I searched for a smiliar cases, and I couldn't figure anyone which had this problem before. Can't use the parallelism tag, because what will be the input for each tool? it should be a fastq file not a directory of fastq files. Neither I would like to run each fastq file in a different workflow - creating a mess. I thought only on two solutions: 1. Implement new datatypes: bed_dir fastq_dir and implements new tool wrappers which will get a folder instead of a file. 2. merge the input files before sending to bowtie, and use parallelism tag to make them be splitted merged again on each tool. Does anyone has any better suggestion? Thanks, Hagai ___ 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] Upload file : auto-detect based on file extension ?
I don't believe you can, although it should be possible to extend
upload to provide that information. However, is there no header you
can use in your filetype to detect it?
--
James Taylor, Assistant Professor, Biology/CS, Emory University
On Mon, Feb 11, 2013 at 10:51 PM, David Angot dav...@intersect.org.au wrote:
Hi,
We are using a proprietary file format in some of our tools.
I successfully added a new data type, but what I would like to do is to use
the auto-detect when uploading the file, just based on the extension of the
file.
My guess is I have to override the sniff() in the datatype class, and test
for the extension ? Somethinkg like that :
if file.endswith('.extension123'):
...
But how do I get the original filename when it was uploaded ?
Thanks,
--
David
___
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[galaxy-dev] Datasets linked into Galaxy do not work
Hi all, I have problems with datasets that were linked into Galaxy data libraries (as Admin: Add datasets, select Upload files from filesystem paths and Link to files without copying to Galaxy). Those files cannot be looked at, downloaded or viewed in a genome browser. Errors in the browser are: The requested URL /datasets/126e6c4f4c2d468e/display/ was not found on this server. The requested URL /library_common/download_dataset_from_folder was not found on this server. An error occurred while accessing: http://galaxy.immunbio.mpg.de/display_application/7108f175b5be4900/igv_bam/local_default/d85d47a3ee6ecd54/data/galaxy_7108f175b5be4900.bam Read error; BinaryCodec in readmode; streamed file (filename not available) I don't see any errors in the log files. We do this kind of linking a lot and everything worked fine in the past. I need to use this feature and need it to work, due to hard disk space and data duplication. Any help is appreciated. Best regards, Sarah ___ 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] Problems linking Data inside Galaxy
Hi, I have followed, carefully, the instructions posted in: http://wiki.galaxyproject.org/Admin/Data%20Integration Yet, despite my best efforts when I get, say all exons from hg19 build and try to their fetch sequences, galaxy tells me that the sequences for hg19 are not there I find this surprising because I have downloaded: rsync://datacache.g2.bx.psu.edu/indexes/ rsync://hgdownload.cse.ucsc.edu/gbdb/ rsync://hgdownload.cse.ucsc.edu/goldenPath/vicPac1/bigZips databases and added the correct paths to the 'alignseq.loc' file Any ideas will be appreciated Thanks --G ___ 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] Overwriting tools directory?
Since I can't find this on any of the wikis: when updating Galaxy through mercurial, is the tools directory affected? Our instance has backups of the directory, but I want to know whether I will have to take care of them when I pull down the latest release. Thanks in advance. -- Amanda Zuzolo Bioengineering Major, George Mason University Metabiome Informatics Group, Environmental Biocomplexity ___ 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] Overwriting tools directory?
Hi Amanda, the tools directory is also tracked and updated in mercurial. But only the tools that are shipped with galaxy. If you have inserted your own tools, they want be affected. If you modified galaxy tools that are part of main galaxy, than you will probably get a merge conflict. But mercurial will tell you that. Kind regards, Bjoern Since I can't find this on any of the wikis: when updating Galaxy through mercurial, is the tools directory affected? Our instance has backups of the directory, but I want to know whether I will have to take care of them when I pull down the latest release. Thanks in advance. ___ 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] Extract genomic DNA job error
So we did the following: Downloaded the data Added the paths to .loc file restarted galaxy We still are getting the following error: 2: Extract Genomic DNA on data 1 empty format: fasta, database: hg19 56 warnings, 1st is: Chromosome by name 'chr22' was not found for build 'hg19'. Skipped 56 invalid lines, 1st is #1, chr22 23487552 23487738 NM_004914_cds_0_0_chr22_23487553_f 0 + My guess is that you .loc file is not set up correctly; you'll need to make sure that there are tab characters—not spaces—separating the columns. If that's not the case, try finding the command line in the galaxy log and running it from the command line (make sure to prepend the command with 'PYTHONPATH=./lib' to get needed Galaxy libraries) and adding debugging statements to see why you twobit file isn't being found. Line 200 of extract_genomic_dna.py may be the key failure point. Finally, please keep all replies on the mailing list for community purposes. Thanks, J. ___ 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] Custom Cheetah filters?
I want to add a filter to strip whitespace and newlines from a text input box so I can pipe the sanitized string to a command. Documentation is a bit sparse (and my Python a bit basic) so does anyone have an example? Perhaps there's a better way of doing it - regex maybe? Any ideas? Thanx, --Russell -- === Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. === ___ 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] Regarding bug card #572 (Trello) and Galaxy Public Server
Regarding this issue ( https://trello.com/card/filter-and-sort-select-tool-not-dealing-with-special-characters-right/506338ce32ae458f6d15e4b3/572 ): No bug is apparent when using an up-to-date local instance of Galaxy (local history on Trello card). However, when using the Galaxy public server the bug is apparent (regular expressions are not registered). So we have come to a few conjectures, 1) The bug has already been fixed in the newest version of Galaxy or 2) Somehow, instantiating the public server is the source of the error (which is unlikely). If one can elucidate any misconceptions (especially about the current version of the Galaxy public server) that we may have that would be great. We would like to resolve this bug. Thank You ___ 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] Fwd: Custom Cheetah filters?
Hi Russell, There may be a better way, but this works for me in the Toolfactory to create space and special character free names? param name=foo type=text value= label=Foo sanitizer invalid_char= valid initial=string.letters,string.digits/ /sanitizer /param On Wed, Feb 13, 2013 at 11:22 AM, Smithies, Russell russell.smith...@agresearch.co.nz wrote: I want to add a filter to strip whitespace and newlines from a text input box so I can pipe the sanitized string to a command. Documentation is a bit sparse (and my Python a bit basic) so does anyone have an example? Perhaps there’s a better way of doing it – regex maybe? ** ** Any ideas? ** ** Thanx, ** ** --Russell -- ** ___ 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] Regarding bug card #572 (Trello) and Galaxy Public Server
Matthew, This is related to the version of grep called by Galaxy. GNU grep presents the issue while BSD grep works as expected. I haven't really dug much, but this could probably be addressed by handling input parameters better in the tool wrapper, if you want to take a look. -Dannon On Feb 12, 2013, at 7:31 PM, Matthew Paul mrp...@g.cofc.edu wrote: Regarding this issue (https://trello.com/card/filter-and-sort-select-tool-not-dealing-with-special-characters-right/506338ce32ae458f6d15e4b3/572): No bug is apparent when using an up-to-date local instance of Galaxy (local history on Trello card). However, when using the Galaxy public server the bug is apparent (regular expressions are not registered). So we have come to a few conjectures, 1) The bug has already been fixed in the newest version of Galaxy or 2) Somehow, instantiating the public server is the source of the error (which is unlikely). If one can elucidate any misconceptions (especially about the current version of the Galaxy public server) that we may have that would be great. We would like to resolve this bug. Thank You ___ 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] tool integration SOAPdenovo
Dear all, Is there a repository where I can finnd SOAPdenovo tool wrappers for Galaxy? I would like to install this tool in our local Galaxy server. Thanks, Jorge ___ 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] tool integration SOAPdenovo
I don't think there's one in a toolshed but someone's clearly done some work on it at http://galaxy.cbiit.cuhk.edu.hk/ Perhaps you may be able to convince them of the many benefits of contributing back to the community by sharing some of their tool code? On Wed, Feb 13, 2013 at 12:32 PM, Jorge Andrade andrade.jo...@gmail.comwrote: Dear all, Is there a repository where I can finnd SOAPdenovo tool wrappers for Galaxy? I would like to install this tool in our local Galaxy server. Thanks, Jorge ___ 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] Fwd: Custom Cheetah filters?
Bodged using string functions :-) set $data = ''.join([line for line in ($seq_source_type.seq_paste.split()) if line[0] != ]) Removes the fasta header line and any white-space so I can pipe sequence directly to blastn. Means users can quickly paste in a bit of sequence for blasting without first having to upload the data to their history. --Russell -- From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Ross Sent: Wednesday, 13 February 2013 1:34 p.m. To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] Fwd: Custom Cheetah filters? Hi Russell, There may be a better way, but this works for me in the Toolfactory to create space and special character free names? param name=foo type=text value= label=Foo sanitizer invalid_char= valid initial=string.letters,string.digits/ /sanitizer /param On Wed, Feb 13, 2013 at 11:22 AM, Smithies, Russell russell.smith...@agresearch.co.nzmailto:russell.smith...@agresearch.co.nz wrote: I want to add a filter to strip whitespace and newlines from a text input box so I can pipe the sanitized string to a command. Documentation is a bit sparse (and my Python a bit basic) so does anyone have an example? Perhaps there's a better way of doing it - regex maybe? Any ideas? Thanx, --Russell -- === Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. === ___ 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] Questions regarding updating the Galaxy on Amazon AWS
Hi Chun-Yuan, Sorry to see you're running running into so much trouble. The reality of the situation is that the Update Galaxy button in CloudMan is currently broken due to the changes in Galaxy that make the updates a rather manual process. For the past several weeks, the team has been working on sorting this out and we are getting closer to having that resolved. The upcoming upgrade will include an update to Galaxy itself, a number of tools, and the machine image. Also, a change in the architecture of the cloud deployment will be necessary to accomplish this. Specifically, galaxyTools and galaxyData volumes (ie, file systems) will be merged into a single file system. As far as mi-deployment goes - it has been deprecated at this point in favor of CloudBioLinux (cloudbiolinux.org). Over the past 6 months or so, the functionality from mi-deployment has been merged with CBL and is the preferred way of building images and tools. As far as getting a volume attached to a specific instance, the AWS console allows you to attach a volume to an instance at a given device. Then, the device becomes available on the attached instance. Note that the device ID may differ from the one you used to attach the device as - this is noted in the AWS console at the time of attaching a volume so you should look for a device with that ID. As far as support goes - unfortunately, we do not have resources to offer phone support. Instead, you should subscribe and send emails to galaxy-dev mailing list (http://lists.bx.psu.edu/listinfo/galaxy-dev). I have CC'd that list now and posting to that list in the future should give the biggest exposure to the questions you may have. Hope this helps. Let us know if you have any more questions, Enis On Tue, Feb 12, 2013 at 9:04 AM, Chun-Yuan Huang hua...@uwm.edu wrote: Dear Dr. Afgan, I am in a lab that focuses on NGS analysis for Zebrafish Bis-seq dataset, and is about to use the Bismark tool (http://www.bioinformatics.** babraham.ac.uk/projects/**bismarkhttp://www.bioinformatics.babraham.ac.uk/projects/bismark) for that purpose. We were very excited to learn that Bismark works in the Galaxy project that you are the main author of, and have been trying to install Bismark into Galaxy for the past few weeks. We have tried and received the following: 1. Start up our own instance on Amazon AWS using ami-da58aab3, galaxy-cloudman-2011-03-22, and following the instructions from Galaxy Wiki to install Bismark manually, including the necessary modifications on the files universe_wsgi.ini, tool_conf.xml, tool_data_table_conf.xml. However, the installed Bismark kept generating error messages that we could not fully resolve. 2. We later noticed that Bismark can be installed from Tool Shed in a rather automatic way. But in order to take advantage of that, we need to update the galaxy system into more recent version in order to have the recent/automatical Tool Shed. Oddly the link in the Cloudman Admin page for Update Galaxy from a provided repository doesn't work for us. So we tried to update the galaxy manually, then the Bismark from Tool Shed. It worked partially, as some tools are functional but not others, including the Bismark. We are in the process of configuring individual tools as well as Bismark. 3. During the frustration, I kept wondering whether there is a more systemic and better documented way of upgrading Galaxy and installing its tools such as Bismark. Although we may be able to figure out all the problems eventually, the time and work spent on it is rather expensive as compared to a stand-alone Linux box. 4. So in looking out for a more systemic and better documented solution, I just came across your site for the mi-deployment ( https://bitbucket.org/afgane/**mi-deploymenthttps://bitbucket.org/afgane/mi-deployment). By reading its overview, it seems this is exactly the solution I have been looking for (sorry for my ignorance on this matter, as I should have tried it from the beginning). I am in the process of trying mi-deployment. But in the meantime, I would like to ask a couple of questions: 1. Is mi-deployment the right track I should be following, or I am still in the wrong place for my situation? Are there more detailed instructions on doing it? Do you have any other suggestions? I consider myself and my group with fair literacy on bioinformatic tools, NGS tools, and how Linux system works (but not experts on it). 2. Per your instruction on mi-deployment, we have established a CloudBioLinux Ubuntu 12.04 instance (version dated to December 2012) and have set environment variables for both access key and secret access key, in addition to using pip to install boto and fabric. We've attempted to create an EBS volume and link it to our EC2 instance, but it does not show up within the /dev directory following a kernel restart. How may we get it to display such that we can then mount it with sudo mount /dev/VOLUME
[galaxy-dev] Circster save just hangs
Hi,I had created a trackster vizualization that had not finished indexing yet, and I decided to change it into a circster visualization.I then added a few more BAM files and tried to save the visualization and now it just hangs there...no errors in the logs so far, but no saving of the visualization either...Thon ___ 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] hg clone link on news brief incorrect
I think the hg clone link on the news brief is incorrect:it states: hgclonehttps://bitbucket.org/galaxy-dist#stableProbably should behgclonehttps://bitbucket.org/galaxy/galaxy-dist#stableThon ___ 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] hg19 reference gnome for Tophat2
I downloaded the entire directory of UCSC for the reference gnome of Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index with the files: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.rev.1.bt2 genome.rev.2.bt2 While adding the reference gnome, I need to edit bowtie2_indices.loc Shall I replace: /orig/path/hg19hg19hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Thanks, Sachit ___ 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] hg19 reference gnome for Tophat2
Also, do I have make all the reference files executable? On Wed, Feb 13, 2013 at 6:39 AM, Sachit Adhikari sachit.techner...@gmail.com wrote: I downloaded the entire directory of UCSC for the reference gnome of Tophat2. It turns out that the Tophat2 and Bowtie2 uses the same reference gnome. I found a directory: Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index with the files: genome.1.bt2 genome.2.bt2 genome.3.bt2 genome.4.bt2 genome.rev.1.bt2 genome.rev.2.bt2 While adding the reference gnome, I need to edit bowtie2_indices.loc Shall I replace: /orig/path/hg19hg19hg19 /depot/data2/galaxy/bowtie2/hg19/hg19 with hg19 hg19hg19 Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index Thanks, Sachit ___ 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] Custom Cheetah filters?
Hi Russell, also keep in mind, that Cheetah is just python. Maybe you can try to do something like that: $text.strip() or str($text).strip() Cheers, Bjoern I want to add a filter to strip whitespace and newlines from a text input box so I can pipe the sanitized string to a command. Documentation is a bit sparse (and my Python a bit basic) so does anyone have an example? Perhaps there’s a better way of doing it – regex maybe? Any ideas? Thanx, --Russell -- === Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. === ___ 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] Preffered way of running a tool on multiple input files
John, that's seems great. I will read this stuff and see if I can use it (The bed format isn't that essential, bowtie can bam instead). If it wont work I will try the other solution which doesn't need to change the galaxy own code (Creating hundreds of workflow run, linking to their outputs and running last workflow with the merging tool - this solution also distribute in a better way). Because galaxy is used a lot on sequencers output, I think someday it should support this kind of jobs internally. When I will have a running solution, I will publish what solution I have used. Its really great to know I'm not the first one to attack this problem. Thanks for the advices. Hagai On Tue, Feb 12, 2013 at 5:42 PM, Joachim Jacob |VIB| joachim.ja...@vib.bewrote: You cannot directly couple different workflows. But you could indeed copy all outputs of the different workflows into one history, and create a separate workflow with your tool to work on all those input files. Cheers, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 02/12/2013 04:31 PM, Hagai Cohen wrote: Thanks for your answer. I figured that there is an option to run a workflow on multiple files, but I can't merge the outputs afterwardsl. I would like the workflow to return one final output. But you gave me another idea. Can I somehow tell one workflow to run on other workflow output? If this can be done, I can run 100 different workflows with bowtie statistics, each working on one fastq file, than run another workflow which gets 100 xls inputs and merge them to one. On Tue, Feb 12, 2013 at 5:20 PM, Joachim Jacob |VIB| joachim.ja...@vib.be mailto:joachim.ja...@vib.be wrote: Hi Hagai, Actually, using a workflow, you are able to select multiple input files, and let the workflow run separately on all input files. I would proceed by creating a data library for all your fastq files, which you can upload via FTP, or via a system directory. You can use a sample of your fastq files to create the steps in a history you want to perform, and extract a workflow out of it. Next, copy all fastq files from a data library in a new history, and run your workflow on the all input files. I hope this helps you further, Joachim Joachim Jacob Rijvisschestraat 120, 9052 Zwijnaarde Tel: +32 9 244.66.34 tel:%2B32%209%20244.66.34 Bioinformatics Training and Services (BITS) http://www.bits.vib.be @bitsatvib On 02/12/2013 04:02 PM, Hagai Cohen wrote: Hi, I'm looking for a preferred way of running Bowtie (or any other tool) on multiple input files and run statistics on the Bowtie output afterwards. The input is a directory of files fastq1..fastq100 The bowtie output should be bed1...bed100 The statistics tool should run on bed1...bed100 and return xls1..xls100 Then I will write a tool which will get xls1..xls100 and merge them to one final output. I searched for a smiliar cases, and I couldn't figure anyone which had this problem before. Can't use the parallelism tag, because what will be the input for each tool? it should be a fastq file not a directory of fastq files. Neither I would like to run each fastq file in a different workflow - creating a mess. I thought only on two solutions: 1. Implement new datatypes: bed_dir fastq_dir and implements new tool wrappers which will get a folder instead of a file. 2. merge the input files before sending to bowtie, and use parallelism tag to make them be splitted merged again on each tool. Does anyone has any better suggestion? Thanks, Hagai __**_ 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/
