Re: [galaxy-user] Variable number of inputs in Workflow (or optional inputs)
Hi Jennifer, Thanks for the reply. However, my question was not about building tools. My question was about building a workflow (using the workflow editor with existing tools), as a user of galaxy. Using the workflow editor, when I create a workflow using a tool that allows a variable number of inputs, it seems that I have to define the number of inputs during workflow creation and not when I run the workflow. I was just asking if it would be feasible to have a variable number of inputs (only defined when a running instance of a workflow is created). It feels to me that the answer is no. Thanks again, Daniel On Mon 05 Mar 2012 05:56:16 PM WET, Jennifer Jackson wrote: Hello Daniel, Examining existing tools that have multiple/optional inputs can be a good way to see how this is done. One example is the tool: NGS: QC and manipulation - Manipulate FASTQ. The 'Manipulate FASTQ' tool source is here: http://bitbucket.org/galaxy/galaxy-central/src/e58a87c91bc4/tools/fastq/ fastq_manipulation.py fastq_manipulation.xml The tool tag set is defined in this wiki; http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax See repeat, conditional, and when for more details and examples. Questions about tools are best sent to the galaxy-...@bx.psu.edu mailing list (the galaxy-user list is primarily for questions about data/tools usages on the main public instance). I am going to forward your question over there so that the development community can add to my reply in case they have a simpler way of doing this or other advice. Best, Jen Galaxy team On 3/5/12 7:32 AM, Daniel Sobral wrote: Hi, I wanted to build a workflow where the first step would be a tool that can have a variable number of inputs (e.g. a series). It seems that I need to predefine apriori the number of inputs to give to the tool. Is there a way to define the number of inputs at runtime? E.g. a series-like input? Thanks, Daniel ___ 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/ ___ 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/
Re: [galaxy-user] Variable number of inputs in Workflow (or optional inputs)
Hi Daniel, My apologies! I misunderstood what your question was about. You are correct, the required inputs are defined when the workflow is created. For tools that accept a variable number of inputs, when that tool is added to a workflow, the run-time parameters, including expected inputs, are defined. Did you have a particular tool in mind? We can ask Dannon for some suggestions/comments if you want to share your ideas about how this sort of processing would flow. I am glad you wrote back. Please send more details if you want and we can try to offer more (better!) help, Best, Jen Galaxy team On 3/6/12 1:01 AM, Daniel Sobral wrote: Hi Jennifer, Thanks for the reply. However, my question was not about building tools. My question was about building a workflow (using the workflow editor with existing tools), as a user of galaxy. Using the workflow editor, when I create a workflow using a tool that allows a variable number of inputs, it seems that I have to define the number of inputs during workflow creation and not when I run the workflow. I was just asking if it would be feasible to have a variable number of inputs (only defined when a running instance of a workflow is created). It feels to me that the answer is no. Thanks again, Daniel On Mon 05 Mar 2012 05:56:16 PM WET, Jennifer Jackson wrote: Hello Daniel, Examining existing tools that have multiple/optional inputs can be a good way to see how this is done. One example is the tool: NGS: QC and manipulation - Manipulate FASTQ. The 'Manipulate FASTQ' tool source is here: http://bitbucket.org/galaxy/galaxy-central/src/e58a87c91bc4/tools/fastq/ fastq_manipulation.py fastq_manipulation.xml The tool tag set is defined in this wiki; http://wiki.g2.bx.psu.edu/Admin/Tools/Tool%20Config%20Syntax Seerepeat,conditional, andwhen for more details and examples. Questions about tools are best sent to the galaxy-...@bx.psu.edu mailing list (the galaxy-user list is primarily for questions about data/tools usages on the main public instance). I am going to forward your question over there so that the development community can add to my reply in case they have a simpler way of doing this or other advice. Best, Jen Galaxy team On 3/5/12 7:32 AM, Daniel Sobral wrote: Hi, I wanted to build a workflow where the first step would be a tool that can have a variable number of inputs (e.g. a series). It seems that I need to predefine apriori the number of inputs to give to the tool. Is there a way to define the number of inputs at runtime? E.g. a series-like input? Thanks, Daniel ___ 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/ -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/wiki/Support ___ 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/
[galaxy-user] April GMOD meeting early registration
Hello, This is a reminder that there is only a little over two days left to get in on early registration for the April 2012 GMOD meeting. In addition to getting a $10 discount on the registration fee, you will be entered in a drawing to get a GMOD coffee cup or T-shirt. There are some very good speakers and topics lined up for the meeting; I'm looking forward to a good one. Please see: http://gmod.org/wiki/April_2012_GMOD_Meeting for more information on the meeting, and to: http://gmod2012.eventbrite.com/ to register for the meeting. I look forward to seeing you next month. Scott -- Scott Cain, Ph. D. scott at scottcain dot net GMOD Coordinator (http://gmod.org/) 216-392-3087 Ontario Institute for Cancer Research ___ 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/
[galaxy-user] Advice on disabling SGE queue on galaxy-cloudman
Hello All- I'd like to launch a galaxy-cloudman head node which does not accept SGE jobs, but as jobs are submitted go to compute nodes (or cause compute node to be added when auto-scale is on). Primarily, this is b/c I'd like to have the head node be a cheaper instance which can run long term, and only fire up more expensive compute nodes as they are actually needed. How would I enable this? Thanks- John ___ 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/
[galaxy-user] FastQC in main galaxy server?
Hi, I've tried FastQC in the main galaxy server and it is throwing me an error: 0 bytes An error occurred running this job: /Traceback (most recent call last): File /galaxy/home/g2main/galaxy_main/tools/rgenetics/rgFastQC.py, line 149, in module assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError: #/ Daniel ___ 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/
[galaxy-user] Tophat Mean Inner Distance between Mate Pairs
Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in Mean Inner Distance between Mate Pairs. In galaxy, we can read the following information: This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter is required for paired end runs. I think the size of fragment (here 300bp) includes not only the length of pair end reads, but also the length of adaptors. so, maybe the Mean Inner Distance between Mate Pairs should be : fragment length - pair end read length - adaptor length. Am I right? or did I miss something? Is it a must to type in the accurate value? Looking forward to your reply JIwen ___ 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/
Re: [galaxy-user] Tophat Mean Inner Distance between Mate Pairs
Hi Jiwen, This is a subject that has me very confused too. This thread at seqanswer didn't help much either: http://seqanswers.com/forums/showthread.php?t=8730 But it does have some good comments on the subject. I did try using the two possible options I can think of: fragment length - pair end read length - adaptor length And: fragment length - pair end read length With the latter I get around 10% increase on properly paired reads. I wonder if Tophat internally takes into account the adapters. Still, it would be nice to get a definitive answer in this subject. Regards, Carlos 2012/3/6 杨继文 jiwenyang0...@126.com: Hi all, When mapping pair end RNA-seq reads using tophat, we need to type in Mean Inner Distance between Mate Pairs. In galaxy, we can read the following information: This is the expected (mean) inner distance between mate pairs. For, example, for paired end runs with fragments selected at 300bp, where each end is 50bp, you should set -r to be 200. There is no default, and this parameter is required for paired end runs. I think the size of fragment (here 300bp) includes not only the length of pair end reads, but also the length of adaptors. so, maybe the Mean Inner Distance between Mate Pairs should be : fragment length - pair end read length - adaptor length. Am I right? or did I miss something? Is it a must to type in the accurate value? Looking forward to your reply JIwen ___ 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/ ___ 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/
[galaxy-user] 'compare two datasets script'?
Hi, I'm wondering if there is a script(s) or set of command lines to download corresponding to the 'Compare two datasets' under 'Join, Subtract and Group' set of tools in Galaxy.I want to run this locally on the command line on many files. I've searched under toolshed but can't seem to find it. Many Thanks, Ken ___ 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/
Re: [galaxy-user] Advice on disabling SGE queue on galaxy-cloudman
Hi John, Theoretically, this is a straightforward task but in reality CloudMan gets in the way of making it stick. Namely, if you are to manually remove the master instance from being an execution host, CloudMan will add it back in the next time a node is added or removed from the cluster, thus negating your manual modification. So, I will add this feature to CloudMan itself but I cannot commit to a date right now. It should be soon though. In the mean time, if you'd like to script this yourself via an add-hoc solution that runs periodically, below is the procedure for manually removing a node from SGE's execution host list: ubuntu@ip-10-204-170-63:~$ sudo -s root@ip-10-204-170-63:~# qhost HOSTNAMEARCH NCPU LOAD MEMTOT MEMUSE SWAPTO SWAPUS --- global - - - - - - - ip-10-204-170-63lx24-amd64 1 1.11 615.2M 161.6M 0.0 0.0 # Remove the host from the list of execution hosts root@ip-10-204-170-63:~# qconf -de ip-10-204-170-63 Host object ip-10-204-170-63 is still referenced in cluster queue all.q. # Edit the configuration of allhosts and remove the host in question. If this is the only host in the list, replace it's name with word NONE root@ip-10-204-170-63:~# qconf -mhgrp @allhosts root@ip-10-204-170-63.ec2.internal modified @allhosts in host group list # Show configuraiton of group allhosts root@ip-10-204-170-63:~# qconf -shgrp @allhosts group_name @allhosts hostlist NONE # The hos is now removed from the list of execution hosts root@ip-10-204-170-63:~# qstat -f root@ip-10-204-170-63:~# On Wed, Mar 7, 2012 at 6:23 AM, John Major john.e.major...@gmail.com wrote: Hello All- I'd like to launch a galaxy-cloudman head node which does not accept SGE jobs, but as jobs are submitted go to compute nodes (or cause compute node to be added when auto-scale is on). Primarily, this is b/c I'd like to have the head node be a cheaper instance which can run long term, and only fire up more expensive compute nodes as they are actually needed. How would I enable this? Thanks- John ___ 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/ ___ 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/
[galaxy-user] Question about plotting circos plot
I wonder if is it possible to visualize mutation data in circular plot termed as circos plot e.g @http://www.eurekalert.org/multimedia/pub/31019.php?from=181881 Any suggestion for an alternative tool will also be appreciated. Thanks Shamsher ___ 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/
