Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy
Thanks! This looks very useful for me. I'm also interested in fleshing out the wrapper, (implementing all possible options, like bowtie's full parameter list), but this should fit my purposes for now. Best regards, Patrick Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Gesendet: Freitag, 18. Januar 2013 04:37 An: Sorn, Patrick Cc: 'galaxy-dev@lists.bx.psu.edu'; 'do...@cshl.edu' Betreff: Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy I have a very basic STAR wrapper that works: https://bitbucket.org/jgoecks/jeremys-code/src/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml?at=default For now, the wrapper does two things: maps RNA-seq reads and identifies chimeric reads/junctions. There are tons of options that aren't yet implemented, but the basics are there. Eventually I'll put the wrapper in the toolshed, but if you want to use it now, you'll need to create your own star_indexes.loc table (identical in structure to the bowtie_indexes.loc table) and add the appropriate entry to tool_data_table_conf.xml This page explains the details of these files: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup If you're interested in helping to flesh out the wrapper, pull requests or patches are welcome. Thanks, J. On Jan 16, 2013, at 7:05 AM, Sorn, Patrick wrote: Hi all, I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if anyone else is working on this? If nobody is, I would do this. Best regards, Patrick Sorn ___ 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] local install problem with fasta manipulation tools?
Hi I hope I have the correct place to ask for assistance. I've been trying to use a local install of Galaxy. I can upload data and convert formats (FASTq to FASTA) but can't use fasta manipulation tools like width formatter or collapse. I am told No such file or directory /bin/sh: fasta_formatter: command not found. I don't see these in the list of tools with dependencies. I've used them frequently on the public website so I don't think this is a problem of my file formats. What am i missing? When I try to send a bug report through the local I get an error that mail is not configured. I assume i have not conducted the installation properly but I can't figure out what i have done wrong. I tried to do the local install because my files on the web version have been sitting for many hours waiting to run. Thanks for any help. Beth ___ 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] Workflows
Hi, I've put together some exempels for activating and using the api. You can find them here: http://geertvandeweyer.zymichost.com/index.php?page=readid=29 Best regards, Geert vandeweyer Op 16-jan.-2013 om 02:52 heeft neil.burd...@csiro.au het volgende geschreven: Hi Sorry if these questions are obvious but I just don’t know how to find the answers. I’m trying to get one of the API examples to work in http://wiki.galaxyproject.org/Learn/API/Examples . I’ve got my API key but how do I get/find the workflow id (f2db41e1fa331b3e in the examples). I’ve created workflow but don’t know how to access this key. Also in the first example it states galaxy_url/api/workflows However I don’t have the “api/workflows” directory structure in my galaxy-dist, do I need to create this? Thanks Neil ___ 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] Problem uploading to Galaxy
Hello, I've encountered a problem uploading some .xlsx files to Galaxy. None of the files I've tried uploading today, via html or ftp, have been successfully uploaded. Instead, the box turns grey and says the Job is waiting to run. If I try to refresh, I get the error: The 'Upload File' tool does not currently support rerunning. Uploading the files to your ftp server and then using Get file gives the same result. Any help or suggestions? Andrew Gorzalski ___ 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: Number of SNPs
Dear Galaxy Team We recently bagan to use galaxy in our lab. I uploaded the whole SNPs several times but the number of them showed difference in every time . Would you please do me a favor and let me know why the number of SNPs differ in every times and what is the reason of this? Best regards, M. Babanejad ___ 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] Galaxy Main cloudlaunch stall
I've searched the list to see if anyone specifically mentions not being able to use the cloud launchhttps://main.g2.bx.psu.edu/cloudlaunch feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user data. However, I can't successfully use the cloud launch page to do the same. I've tried letting it create a new security group as well as using a pre-existing security group. Also, I've then deleted all security groups to see if it would create one, which it did not. Similarly, I tried creating a new access key pair, with no further success. I make it through the process of entering the key ID and secret key, it pulls existing security group information into the drop-down selector, and I give a cluster name and password and submit the form. Then it just stalls forever. No new security groups and no EC2 instances launched. What is the state of this tool? Thanks. ___ 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] UCSC Data Browser
Hello, Is anyone having trouble with the UCSC data browser? I got the following from one of my users: Hi guys, I try to fetch data from UCSC browser. A summary of my query shows that I am getting what I ask for, but when I Send the data to Galaxy I am returned to the channing galaxy home page and the data never appears in the history. When I use public instance, it all works. Not sure where the disconnect is. Thanks Any help would be appreciated. -Rob ___ 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 Main cloudlaunch stall
Cloudlaunch on the main public instance is fully supported and should work fine -- I use it regularly for launching instances without issue. There was a brief EC2 API outage yesterday (on the Amazon end) that caused intermittent errors to all users of the API (including cloudlaunch), but that should be resolved now. Creating security groups and selecting (or creating, if necessary) an access key should be possible -- since it's not even getting that far I'm wondering if there isn't a Javascript error or something preventing the form submission. What browser are you using, and do you see any errors? -Dannon On Jan 17, 2013, at 5:11 PM, Matthew Shirley mshir...@jhmi.edu wrote: I've searched the list to see if anyone specifically mentions not being able to use the cloud launch feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user data. However, I can't successfully use the cloud launch page to do the same. I've tried letting it create a new security group as well as using a pre-existing security group. Also, I've then deleted all security groups to see if it would create one, which it did not. Similarly, I tried creating a new access key pair, with no further success. I make it through the process of entering the key ID and secret key, it pulls existing security group information into the drop-down selector, and I give a cluster name and password and submit the form. Then it just stalls forever. No new security groups and no EC2 instances launched. What is the state of this tool? Thanks. ___ 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] Integration of STAR Aligner v2.2.0c into Galaxy
Do you know how I can read in gzipped FASTQ files in the STAR wrapper without writing an external Python script or the like? Thanks, Patrick Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Gesendet: Freitag, 18. Januar 2013 04:37 An: Sorn, Patrick Cc: 'galaxy-dev@lists.bx.psu.edu'; 'do...@cshl.edu' Betreff: Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy I have a very basic STAR wrapper that works: https://bitbucket.org/jgoecks/jeremys-code/src/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml?at=default For now, the wrapper does two things: maps RNA-seq reads and identifies chimeric reads/junctions. There are tons of options that aren't yet implemented, but the basics are there. Eventually I'll put the wrapper in the toolshed, but if you want to use it now, you'll need to create your own star_indexes.loc table (identical in structure to the bowtie_indexes.loc table) and add the appropriate entry to tool_data_table_conf.xml This page explains the details of these files: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup If you're interested in helping to flesh out the wrapper, pull requests or patches are welcome. Thanks, J. On Jan 16, 2013, at 7:05 AM, Sorn, Patrick wrote: Hi all, I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if anyone else is working on this? If nobody is, I would do this. Best regards, Patrick Sorn ___ 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] Workflows
Geert, this is great stuff! One small correction -- the API is enabled by default as of revision 7022:8376ad08ae41 (April 2012). -Dannon On Jan 16, 2013, at 1:17 AM, Geert Vandeweyer geertvandewe...@gmail.com wrote: Hi, I've put together some exempels for activating and using the api. You can find them here: http://geertvandeweyer.zymichost.com/index.php?page=readid=29 Best regards, Geert vandeweyer Op 16-jan.-2013 om 02:52 heeft neil.burd...@csiro.au het volgende geschreven: Hi Sorry if these questions are obvious but I just don’t know how to find the answers. I’m trying to get one of the API examples to work in http://wiki.galaxyproject.org/Learn/API/Examples . I’ve got my API key but how do I get/find the workflow id (f2db41e1fa331b3e in the examples). I’ve created workflow but don’t know how to access this key. Also in the first example it states galaxy_url/api/workflows However I don’t have the “api/workflows” directory structure in my galaxy-dist, do I need to create this? Thanks Neil ___ 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/ ___ 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/ ___ 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] missing eye icon on running jobs…
The display icon has been re-enabled in revision 8634:b9d44cf4b68e. Thanks for the catch/feedback. On Wed, Jan 9, 2013 at 12:00 PM, Langhorst, Brad langho...@neb.com wrote: In some cases (e.g. mira) it's nice to be able to follow what's going on in the log file… Does anybody else miss being able to view files as they're running? brad -- Brad Langhorst langho...@neb.com ___ 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] missing eye icon on running jobs…
On Wed, Jan 9, 2013 at 5:00 PM, Langhorst, Brad langho...@neb.com wrote: In some cases (e.g. mira) it's nice to be able to follow what's going on in the log file… Does anybody else miss being able to view files as they're running? brad I remember specifically testing that I could read MIRA's log in Galaxy as it was being generated - thanks for reporting this - I'm glad to know that will work in Galaxy again soon :) Peter ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy Main cloudlaunch stall
Hi Matthew, Would you like to try out what we put together for modENCODE DCC? Please see the README file in the docs folder at https://github.com/modENCODE-DCC/Galaxy Thanks, Q On Fri, Jan 18, 2013 at 10:17 AM, Dannon Baker dannonba...@me.com wrote: Cloudlaunch on the main public instance is fully supported and should work fine -- I use it regularly for launching instances without issue. There was a brief EC2 API outage yesterday (on the Amazon end) that caused intermittent errors to all users of the API (including cloudlaunch), but that should be resolved now. Creating security groups and selecting (or creating, if necessary) an access key should be possible -- since it's not even getting that far I'm wondering if there isn't a Javascript error or something preventing the form submission. What browser are you using, and do you see any errors? -Dannon On Jan 17, 2013, at 5:11 PM, Matthew Shirley mshir...@jhmi.edu wrote: I've searched the list to see if anyone specifically mentions not being able to use the cloud launch feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user data. However, I can't successfully use the cloud launch page to do the same. I've tried letting it create a new security group as well as using a pre-existing security group. Also, I've then deleted all security groups to see if it would create one, which it did not. Similarly, I tried creating a new access key pair, with no further success. I make it through the process of entering the key ID and secret key, it pulls existing security group information into the drop-down selector, and I give a cluster name and password and submit the form. Then it just stalls forever. No new security groups and no EC2 instances launched. What is the state of this tool? Thanks. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] galaxy using EC2 spot pricing
Does anyone have any experience running Galaxy using Amazon's EC2 spot pricing? It seems like that could save a lot of money as compared to on-demand pricing, and it appears that there are ways to mix on-demand and spot instances within one processing cluster: http://aws.amazon.com/ec2/spot-and-science/ ___ 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 using EC2 spot pricing
While it isn't bulletproof yet (restarting jobs that fail due to spot instance reclaims, etc), Cloudman (usegalaxy.org/cloud) does currently have support for running worker nodes as spot instances. When you go to add nodes, just click Use Spot Instances, and add your spot price. For obvious reasons, you wouldn't want the head node of your cluster to be a spot instance, use a normal one for that. -Dannon On Jan 18, 2013, at 11:58 AM, Andrew Norman anorma...@gmail.com wrote: Does anyone have any experience running Galaxy using Amazon's EC2 spot pricing? It seems like that could save a lot of money as compared to on-demand pricing, and it appears that there are ways to mix on-demand and spot instances within one processing cluster: http://aws.amazon.com/ec2/spot-and-science/ ___ 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] Problem uploading to Galaxy
Hi Andrew, If this was on Main at Penn State, there was a problem with uploads that we believe has now been resolved. Dave C On Wed, Jan 16, 2013 at 5:21 PM, Andrew Gorzalski gorzal...@gmail.comwrote: Hello, I've encountered a problem uploading some .xlsx files to Galaxy. None of the files I've tried uploading today, via html or ftp, have been successfully uploaded. Instead, the box turns grey and says the Job is waiting to run. If I try to refresh, I get the error: The 'Upload File' tool does not currently support rerunning. Uploading the files to your ftp server and then using Get file gives the same result. Any help or suggestions? Andrew Gorzalski ___ 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/ -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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 Main cloudlaunch stall
Should definitely be stable enough to use in a classroom and that it isn't working for you is definitely unexpected; it's the only way I've launched instances for many months now. I'm digging through logs to see if I can find any indication of why your particular requests are having issues. On Jan 18, 2013, at 12:33 PM, Matthew Shirley mshir...@jhmi.edu wrote: Thanks, Quang. That's not exactly what I'm looking for. My motivation is to teach an entire class how to start a Galaxy cluster on their own, with minimal knowledge of AWS or systems administration. The cloudlaunch feature on the main psx site seems to fit this purpose exactly, but does not work reliably for me. I've just tried using Chrome 24.0 with no success. I'm using no browser plugins, and this is a clean installation with javascript enabled. The cloudlaunch page just sits there and tells me Launch Pending, please be patient. and I have - it's been over an hour. Any help figuring this out is appreciated. If this feature is just not mature enough to use in a classroom, that would be an acceptable answer as well. On Jan 18, 2013, at 11:40 AM, Quang Trinh quang.tr...@gmail.com wrote: Hi Matthew, Would you like to try out what we put together for modENCODE DCC? Please see the README file in the docs folder at https://github.com/modENCODE-DCC/Galaxy Thanks, Q On Fri, Jan 18, 2013 at 10:17 AM, Dannon Baker dannonba...@me.com wrote: Cloudlaunch on the main public instance is fully supported and should work fine -- I use it regularly for launching instances without issue. There was a brief EC2 API outage yesterday (on the Amazon end) that caused intermittent errors to all users of the API (including cloudlaunch), but that should be resolved now. Creating security groups and selecting (or creating, if necessary) an access key should be possible -- since it's not even getting that far I'm wondering if there isn't a Javascript error or something preventing the form submission. What browser are you using, and do you see any errors? -Dannon On Jan 17, 2013, at 5:11 PM, Matthew Shirley mshir...@jhmi.edu wrote: I've searched the list to see if anyone specifically mentions not being able to use the cloud launch feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user data. However, I can't successfully use the cloud launch page to do the same. I've tried letting it create a new security group as well as using a pre-existing security group. Also, I've then deleted all security groups to see if it would create one, which it did not. Similarly, I tried creating a new access key pair, with no further success. I make it through the process of entering the key ID and secret key, it pulls existing security group information into the drop-down selector, and I give a cluster name and password and submit the form. Then it just stalls forever. No new security groups and no EC2 instances launched. What is the state of this tool? Thanks. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
[galaxy-dev] login problems
Hello, I am trying to connect to ftp with my username and password that I registered in galaxy. I am doing this through Filezilla. I am getting the error could not connect to server. Do you know what the problem is, please? Thank you. Eleanne ___ 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] Colon in drmout and drmerr file names creates issues with Torque and DRMAA when using 'use_tasked_jobs'.
Hi All, Thanks to this email[1] from Peter Cock I was able to find what was causing the error I initially described here[2]. I also now have a theory of why this is happening. My unconfirmed guess. When a colon is present in the standard output or standard error file, someone betweent Galaxy, python-drmaa, pbs-drmaa, Torque or Maui recognize this as a scp syntax, like: user@host:/path/to/file And then choose to at 'galaxy@' in from of what is really a filesystem path. This is why I'm seeing this kind of error: Unable to copy file /var/spool/torque/spool/1013.head.OU to galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9 /task_0/9:1.drmout *** error from copy cp: cannot create regular file `galaxy@/local/opt/galaxy/galaxy-dist.8082/database/job_working_directory/000/9/task_0/9:1.drmout': No such file or directory *** end error output Output retained on that host in: /var/spool/torque/undelivered/1013.head.OU By using Peter's .replace(:, _) trick on lib/galaxy/jobs/runners/drmaa.py I was able to make this issue go away. As Peter mention this is a very dirty fix and I'm sure there has to be a much cleaner way of fixing this issue. [1]http://dev.list.galaxyproject.org/Galaxy-with-Univa-Grid-Engine-UGE-instead-of-SGE-td4657848.html [2]http://dev.list.galaxyproject.org/Issue-when-enabling-use-tasked-jobs-with-torque-and-nfs-td4657294.html I'll be opening a ticket on Trello to follow the progress on this issue. Regards, Carlos ___ 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] local install problem with fasta manipulation tools?
I hope I have the correct place to ask for assistance. Yes, this list is a great place to ask questions about local Galaxy instances. I've been trying to use a local install of Galaxy. I can upload data and convert formats (FASTq to FASTA) but can't use fasta manipulation tools like width formatter or collapse. I am told No such file or directory /bin/sh: fasta_formatter: command not found. I don't see these in the list of tools with dependencies. I've used them frequently on the public website so I don't think this is a problem of my file formats. What am i missing? When I try to send a bug report through the local I get an error that mail is not configured. You need to install analysis tools that you want to use with Galaxy. The tool shed will help with some tools (see Admin -- Tool sheds -- search and browse tool sheds), but others you'll have to install yourself by downloading them and adding them to your PATH. I tried to do the local install because my files on the web version have been sitting for many hours waiting to run. There was a problem with our public server's cluster, but it's been fixed and jobs should be running more quickly now. Best, 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/
Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy
The wrapper isn't set up to support gzipped FASTQ because Galaxy unzips datasets when they are uploaded, so the wrapper won't ever see a gzipped FASTQ dataset. We plan to dataset gzip support to Galaxy in the future. J. On Jan 18, 2013, at 10:21 AM, Sorn, Patrick wrote: Do you know how I can read in gzipped FASTQ files in the STAR wrapper without writing an external Python script or the like? Thanks, Patrick Von: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Gesendet: Freitag, 18. Januar 2013 04:37 An: Sorn, Patrick Cc: 'galaxy-dev@lists.bx.psu.edu'; 'do...@cshl.edu' Betreff: Re: [galaxy-dev] Integration of STAR Aligner v2.2.0c into Galaxy I have a very basic STAR wrapper that works: https://bitbucket.org/jgoecks/jeremys-code/src/fa1930a689b8e2f6b59cc1706e5ba0ed8ad357be/galaxy/tool-wrappers/star.xml?at=default For now, the wrapper does two things: maps RNA-seq reads and identifies chimeric reads/junctions. There are tons of options that aren't yet implemented, but the basics are there. Eventually I'll put the wrapper in the toolshed, but if you want to use it now, you'll need to create your own star_indexes.loc table (identical in structure to the bowtie_indexes.loc table) and add the appropriate entry to tool_data_table_conf.xml This page explains the details of these files: http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup If you're interested in helping to flesh out the wrapper, pull requests or patches are welcome. Thanks, J. On Jan 16, 2013, at 7:05 AM, Sorn, Patrick wrote: Hi all, I want to integrate STAR Aligner v2.2.0c into Galaxy and I was wondering if anyone else is working on this? If nobody is, I would do this. Best regards, Patrick Sorn ___ 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 Main cloudlaunch stall
Thanks. The requests will be coming from kennedykrieger.org. On Jan 18, 2013, at 12:36 PM, Dannon Baker dannonba...@me.com wrote: Should definitely be stable enough to use in a classroom and that it isn't working for you is definitely unexpected; it's the only way I've launched instances for many months now. I'm digging through logs to see if I can find any indication of why your particular requests are having issues. On Jan 18, 2013, at 12:33 PM, Matthew Shirley mshir...@jhmi.edu wrote: Thanks, Quang. That's not exactly what I'm looking for. My motivation is to teach an entire class how to start a Galaxy cluster on their own, with minimal knowledge of AWS or systems administration. The cloudlaunch feature on the main psx site seems to fit this purpose exactly, but does not work reliably for me. I've just tried using Chrome 24.0 with no success. I'm using no browser plugins, and this is a clean installation with javascript enabled. The cloudlaunch page just sits there and tells me Launch Pending, please be patient. and I have - it's been over an hour. Any help figuring this out is appreciated. If this feature is just not mature enough to use in a classroom, that would be an acceptable answer as well. On Jan 18, 2013, at 11:40 AM, Quang Trinh quang.tr...@gmail.com wrote: Hi Matthew, Would you like to try out what we put together for modENCODE DCC? Please see the README file in the docs folder at https://github.com/modENCODE-DCC/Galaxy Thanks, Q On Fri, Jan 18, 2013 at 10:17 AM, Dannon Baker dannonba...@me.com wrote: Cloudlaunch on the main public instance is fully supported and should work fine -- I use it regularly for launching instances without issue. There was a brief EC2 API outage yesterday (on the Amazon end) that caused intermittent errors to all users of the API (including cloudlaunch), but that should be resolved now. Creating security groups and selecting (or creating, if necessary) an access key should be possible -- since it's not even getting that far I'm wondering if there isn't a Javascript error or something preventing the form submission. What browser are you using, and do you see any errors? -Dannon On Jan 17, 2013, at 5:11 PM, Matthew Shirley mshir...@jhmi.edu wrote: I've searched the list to see if anyone specifically mentions not being able to use the cloud launch feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user data. However, I can't successfully use the cloud launch page to do the same. I've tried letting it create a new security group as well as using a pre-existing security group. Also, I've then deleted all security groups to see if it would create one, which it did not. Similarly, I tried creating a new access key pair, with no further success. I make it through the process of entering the key ID and secret key, it pulls existing security group information into the drop-down selector, and I give a cluster name and password and submit the form. Then it just stalls forever. No new security groups and no EC2 instances launched. What is the state of this tool? Thanks. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Galaxy Main cloudlaunch stall
Thanks, Quang. That's not exactly what I'm looking for. My motivation is to teach an entire class how to start a Galaxy cluster on their own, with minimal knowledge of AWS or systems administration. The cloudlaunch feature on the main psx site seems to fit this purpose exactly, but does not work reliably for me. I've just tried using Chrome 24.0 with no success. I'm using no browser plugins, and this is a clean installation with javascript enabled. The cloudlaunch page just sits there and tells me Launch Pending, please be patient. and I have - it's been over an hour. Any help figuring this out is appreciated. If this feature is just not mature enough to use in a classroom, that would be an acceptable answer as well. On Jan 18, 2013, at 11:40 AM, Quang Trinh quang.tr...@gmail.commailto:quang.tr...@gmail.com wrote: Hi Matthew, Would you like to try out what we put together for modENCODE DCC? Please see the README file in the docs folder at https://github.com/modENCODE-DCC/Galaxy Thanks, Q On Fri, Jan 18, 2013 at 10:17 AM, Dannon Baker dannonba...@me.com wrote: Cloudlaunch on the main public instance is fully supported and should work fine -- I use it regularly for launching instances without issue. There was a brief EC2 API outage yesterday (on the Amazon end) that caused intermittent errors to all users of the API (including cloudlaunch), but that should be resolved now. Creating security groups and selecting (or creating, if necessary) an access key should be possible -- since it's not even getting that far I'm wondering if there isn't a Javascript error or something preventing the form submission. What browser are you using, and do you see any errors? -Dannon On Jan 17, 2013, at 5:11 PM, Matthew Shirley mshir...@jhmi.edu wrote: I've searched the list to see if anyone specifically mentions not being able to use the cloud launch feature on the main public instance, but no one seems to address it. I have no trouble launching Galaxy-cloudman using an AMI and pasting in my own user data. However, I can't successfully use the cloud launch page to do the same. I've tried letting it create a new security group as well as using a pre-existing security group. Also, I've then deleted all security groups to see if it would create one, which it did not. Similarly, I tried creating a new access key pair, with no further success. I make it through the process of entering the key ID and secret key, it pulls existing security group information into the drop-down selector, and I give a cluster name and password and submit the form. Then it just stalls forever. No new security groups and no EC2 instances launched. What is the state of this tool? Thanks. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
Re: [galaxy-dev] Bug in handling user job limits (due to dynamic job runner code?)
Just an update on this issue. Upon further investigation, it looks like the dynamic job runner code in commit 6f3b4e8 broke this. I haven't been able to parse through everything going on yet to propose a fix, but I've discovered two things: 1) Moving the self.__clear_user_job_count() call outside of the if block, does indeed fix that issue 2) Fixing that leads the __check_user_jobs method to fail since it does not check `self.track_jobs_in_database`, but instead assumes that jobs are in the database, resulting in a different exception regarding invalid columns. Lance Parsons wrote: I submitted a trello ticket [(https://trello.com/c/6vxkqdjT) regarding this, but wanted to make sure I brought it to someone's attention (it's causing me some queue issues with my instance of galaxy). When registered_user_job_limit and anonymous_user_job_limit are set in universe.wsgi jobs cannot be run, instead the following error occurs: galaxy.jobs.handler ERROR 2012-12-04 12:44:51,869 failure running job 22396 Traceback (most recent call last): File /data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py, line 183, in __monitor_step job_state = self.__check_if_ready_to_run( job ) File /data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py, line 253, in __check_if_ready_to_run state = self.__check_user_jobs( job ) File /data/local/galaxy/galaxy-prod/lib/galaxy/jobs/handler.py, line 274, in __check_user_jobs if not self.user_job_count: AttributeError: 'JobHandlerQueue' object has no attribute 'user_job_count' Commenting out the lines for registered_user_job_limit and anonymous_user_job_limit in universe.wsgi allows job to be queue one again. It looks like this is due to the fact that `self.__clear_user_job_count()` on line 159 of `handler.py` is only called when jobs are tracked in the database. If jobs are not tracked in the database (as in my case), the error occurs. Perhaps the fix would be to simply move the call outside the `if` block. It appears this was broken in the 2012-11-13 revision (73e05bc). -- Lance Parsons - Scientific Programmer 134 Carl C. Icahn Laboratory Lewis-Sigler Institute for Integrative Genomics Princeton University ___ 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] login problems
Hi Eleanne, Take a look at http://wiki.galaxyproject.org/FTPUpload. FTP also needs to be enabled on the Galaxy server you are using. Which server are you trying to connect to? Thanks, Dave C. On Fri, Jan 18, 2013 at 10:42 AM, Solorzano, Eleanne eleanne.solorz...@unh.edu wrote: Hello, I am trying to connect to ftp with my username and password that I registered in galaxy. I am doing this through Filezilla. I am getting the error could not connect to server. Do you know what the problem is, please? Thank you. Eleanne ___ 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/ -- http://galaxyproject.org/wiki/GCC2012http://galaxyproject.org/ http://getgalaxy.org/ http://usegalaxy.org/ http://wiki.galaxyproject.org/ ___ 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/
