Re: [galaxy-user] Blast2GO local instance Re: Table with gene count reads
On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Mar 24, 2012, at 7:30 AM, Peter Cock wrote: Have you seen the README file that comes with the Blast2GO wrapper? Perhaps the 'install from toolshed' could be tweaked to make this kind of documentation more visible... If you are installing a single repository that contains a file named one of (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of the file will be displayed on the tool panel section selection page. An example using the antismash repository on the main tool shed is below. This new feature is available in change set revision 6945:5ea04ccb61e8, which is currently running on the Galaxy tool shed and our central development repository. It will be available in the next Galaxy distribution. Great. In this case I've actually called the file blast2go.txt (to match the use of blast2go.xml and blast2go.py). I didn't want to use a generic name like README since there could be other tools installed in the same folder (this predates the auto-install system). Is this naming pattern common used enough to justify including in the Galaxy Tool Shed code for spotting a README file? Care must be taken when following instructions in README files since some of the information may be outdated. For example, the Galaxy functional test framework was recently enhanced to support testing tools included in installed repositories, but I've seen some README files currently in repositories that instruct installers to move test data to the Galaxy installation environment, which is no longer necessary. Some of my tools' README files will need a little clarification following those changes to Galaxy. Thanks, Peter ___ 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] Blast2GO local instance Re: Table with gene count reads
On Apr 3, 2012, at 6:07 AM, Peter Cock wrote: On Mon, Apr 2, 2012 at 6:41 PM, Greg Von Kuster g...@bx.psu.edu wrote: On Mar 24, 2012, at 7:30 AM, Peter Cock wrote: Have you seen the README file that comes with the Blast2GO wrapper? Perhaps the 'install from toolshed' could be tweaked to make this kind of documentation more visible... If you are installing a single repository that contains a file named one of (case is ignored) readme, readme.txt, read_me, read_me.txt, the contents of the file will be displayed on the tool panel section selection page. An example using the antismash repository on the main tool shed is below. This new feature is available in change set revision 6945:5ea04ccb61e8, which is currently running on the Galaxy tool shed and our central development repository. It will be available in the next Galaxy distribution. Great. In this case I've actually called the file blast2go.txt (to match the use of blast2go.xml and blast2go.py). I didn't want to use a generic name like README since there could be other tools installed in the same folder (this predates the auto-install system). Is this naming pattern common used enough to justify including in the Galaxy Tool Shed code for spotting a README file? Since the read me file contains instructions for installing the tools in the repository, would it be better to assume only 1 installation file that includes different instructions per contained tool if necessary? If multiple read me files are allowed per repository, they would all have to be merged together with the entire content displayed on the tool panel section selection screen anyway, so allowing only a single file would be better. The read me in your blast2go repository is named blast2go.txt, so I suppose we could expand the read me file name list to include repository name.txt. I'll do this. Care must be taken when following instructions in README files since some of the information may be outdated. For example, the Galaxy functional test framework was recently enhanced to support testing tools included in installed repositories, but I've seen some README files currently in repositories that instruct installers to move test data to the Galaxy installation environment, which is no longer necessary. Some of my tools' README files will need a little clarification following those changes to Galaxy. My next big feature will be supporting installation of tool dependencies automatically with the repository contents, so keep that in mind if you're making changes to install instructions. This enhancement will take a bit of time. Thanks, Peter ___ 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] Cloudman - Problem starting shared cluster
How do I know which snapshot is the appropriate one? The folder Dannon mentioned seems to be missing. I swear this sharestring worked when I tested it two months ago. I can't imagine what happened. -Greg On Mon, Apr 2, 2012 at 6:48 PM, Enis Afgan enis.af...@irb.hr wrote: Along with the folder structure Dannon is referring to, an appropriate EBS snapshot should exits under your account. This is available from the EC2 tab on the AWS console. As far as the complete logs goes, on CloudMan's admin page, there is a link to the full CloudMan log (alternatively, the same log is available under /mnt/cm/paster.log on the instance itself). Enis On Tue, Apr 3, 2012 at 5:02 AM, Dannon Baker dannonba...@me.com wrote: The first thing to check would be to verify that that the bucket and contents exist in your account. Use the AWS console to log in, go to the S3 tab, and look for the bucket 'cm-31bf91279e41769ff78af22c1a276ece' and verify the /shared/2012-01-12--18-03 folder structure exists. -Dannon On Apr 2, 2012, at 12:40 PM, mailing list wrote: Hi guys, I'm still stuck on this :-(. Are there any log files I could look at to get more details? I'm definitely willing to dive in an get to the bottom of this issue. Can anyone recommend a starting point? Thanks again, Greg On Mon, Apr 2, 2012 at 9:01 AM, mailing list margeem...@gmail.com wrote: Hi guys, After launching Cloudman on the Initial Cluster Configuration dialog I selected the Share-an-Instance Cluster option and put in this share string: cm-31bf91279e41769ff78af22c1a276ece/shared/2012-01-12--18-03 But after that I see this message in the log: 12:52:19 - Problem copying shared cluster configuration files. Cannot continue with shared cluster initialization. And nothing else happens after that. The applications status stays yellow, and disk status says 0/0. Here is some more information about the run: That sharestring is from a share I made in January. It worked when I last tested it in January. I launched via the BioCloudCentral wep app. Other run information: Instance ID i-8523cee2 Image ID (AMI) ami-500cd139 Security group CloudMan Key pair cloudman_key_pair Placement (zone) us-east-1b Let me know what other information would be helpful. Thanks, Greg ___ 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/ ___ 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] Cloudman - Problem starting shared cluster
Thanks Brad. Your last point sounds suspiciously like something I would do ... So whenever I share I can terminate my instance but I shouldn't remove any data? Is that correct? Thanks, Greg On Tue, Apr 3, 2012 at 9:18 AM, Brad Chapman chapm...@50mail.com wrote: Greg; How do I know which snapshot is the appropriate one? The Amazon console displays the description for snapshots. They should have a string like: CloudMan share-a-cluster cluster_name: cm-31bf91279e41769ff78af22c1a276ec The folder Dannon mentioned seems to be missing. I swear this sharestring worked when I tested it two months ago. I can't imagine what happened. CloudMan can't re-build the shared instance without the EC2 folder, since this contains all of the metadata. If you deleted it since last testing it, that would explain the errors you're seeing. If it wasn't manually deleted, it's possible you may have deleted the entire cm-31bf91279e41769ff78af22c1a276ec bucket at some point when shutting down another CloudMan instance and checking Remove all data. I've made this mistake in the past, forgetting that I had shared data in that cluster_name. Hope this helps, Brad ___ 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] Disk space quota Issue
Hello Ateeq, You are correct, the disk space for accounts is a fixed amount on the public main Galaxy instance. Permanently deleting (sometimes called Purge/purging in the UI) datasets and histories is the method to use to create more working space. http://wiki.g2.bx.psu.edu/Main#User_data_and_job_quotas Best, Jen Galaxy team On 4/2/12 12:30 PM, Ateequr Rehman wrote: Dear Administartor My disk space quote is full, is their any way to increase it,or only way is delete some files... Best Ateeq Ateequr Rehman House No. 2 ground floor Blauenstr. 10 79115 Freiburg im Breisgau ** ___ 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] Galaxy Server running error in fetching sequences
Hong: I'm forwarding this to our official user mailing list. Please, use it in the future for your inquiries. Thanks! anton Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org On Apr 3, 2012, at 4:37 PM, xu hong wrote: Hi Anton, I'm a biological student using Galaxy sever to fetch sequences in fasta format for our bioinformatics data analysis. First, I uploaded our BED file(I think there is no significant difference from the GFF format defined in Galaxy/UCSC), and then use Fetch Sequences function in Galaxy Server. However, I got the following error: 2: Extract Genomic DNA on data 1 0 bytes An error occurred running this job: Traceback (most recent call last): File /galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py, line 288, in module f __name__ == __main__: __main__() File /galaxy/home/g2main/galaxy_main/tools/extract/extract_genomic_dna.py Could you help me configure out what's wrong with my analysis or could you get the fasta file I want for me? Attached is the BED file(based on hg18) I uploaded to Galaxy server in psu. Thanks. Beg your reply. Best Hong Xu Zhejiang University,China IGGPart2.rar ___ 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] FASTQ joiner fails to join PE data.
Hi, I have HiSeq2000 paired end sequence data in two separate FASTQ files. I need to filter the low quality scored sequences from my data to have a good assembly. So I decided to join the PE reads and then filter the low quality sequences in Galaxy. To do this first I groomed the data using FASTQ groomer where I kept Sanger as Input FASTQ quality scores type. Then I tried to join the PE sequences using FASTQ joiner. However the FASTQ joiner did not join the PE sequences but only shown the failure Info as follows *FASTQ joiner on data 8 and data 9* 0 bytes format: fastqsanger, database: ?https://main.g2.bx.psu.edu/datasets/d08dd42f0e2ed22b/edit Info: There were 400 known sequence reads not utilized. Joined 0 of 400 read pairs (0.00%). I am a new user and I have no idea where I am going wrong. Please suggest me how to overcome this problem. Thanks. -- ** ___ 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/
