[galaxy-user] genome for Stenotrophomans
Dear Galaxy AdministratorI am analysing transcriptome and genome of clinical isolatesStenotrophomonasmaltophilia, would be highly obliged if you could please upload Stenotrophomonas maltophilia K279 and Stenotrophomonas maltophilia R551-3 genome acccesion numbers at NCBI are as following Stenotrophomonas maltophilia K279 (Accession AM743169) Stenotrophomonas maltophilia R551-3, complete genome Accession: CP00 Thanking you all in advance Ateequr Rehman___ 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] Unable to download files from barcode splitter (from public Galaxy)
Hi, I run Barcode Splitter (from public Galaxy server) and am unable to download the text files generated by the barcode splitter, got an error message which says ' Could not find 'FASTQ_Groomer_on_data_1__V1.txt' on the extra files path /galaxy/main_pool/pool2/files/003/610/dataset_3610002_files/FASTQ_Groomer_on_data_1__V1.txt. The run was Ok (green colour) but yet i was unable to download the text files. Could you please advise? Also, I wonder if you could help regarding the local Galaxy.. I used VirtualBox to install the local copy, and installed according to the instructions as in the website, command as hg clone https://; The setup was smooth and went OK. The problem starts when I run the local Galaxy using real data. I could upload the files, but have problems with the fastQC and barcode splitter, I could not proceed any further since these two operations could not be run...The error messages are: FastQC An error occurred running this job: Traceback (most recent call last): File /home/Desktop/galaxy-dist/tools/rgenetics/rgFastQC.py, line 141, in module assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError Barcode Splitter An error occurred running this job: /home/Desktop/galaxy-dist/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh: line 65: fastx_barcode_splitter.pl: command not found gzip: stdout: Broken pipe Can anyone help me please? I installed the local Galaxy but could not proceed further. I then used the public Galaxy but could not download the files Hope to hear from you. Thanks very much. Best regards Alicia ___ 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] Alignments tutorial now working
Hello, I was trying to figure out how to extract Alignments, and it appears that the video tutorial for that is not working (dead link). Thought I¹d report it, and I hope this is the right email address to send this report to. Thanks. Vikram The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message.___ 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] Alignments tutorial now working
Hi Vikram, Would you be able to email back the exact location of the Galaxy Page or wiki page that this screencast is linked from? If more than one screencast is this location, please note the exact name of the one with a problem, to make sure we are looking at the same thing. I'll take a look and (hopefully) determine the root cause of the issue. Thanks for reporting! This is a great email to use for reporting issues found in the UI. Best, Jen Galaxy On 1/13/12 12:33 PM, Paralkar, Vikram wrote: Hello, I was trying to figure out how to extract Alignments, and it appears that the video tutorial for that is not working (dead link). Thought I’d report it, and I hope this is the right email address to send this report to. Thanks. Vikram The information contained in this e-mail message is intended only for the personal and confidential use of the recipient(s) named above. If the reader of this message is not the intended recipient or an agent responsible for delivering it to the intended recipient, you are hereby notified that you have received this document in error and that any review, dissemination, distribution, or copying of this message is strictly prohibited. If you have received this communication in error, please notify us immediately by e-mail, and delete the original message. ___ 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/
Re: [galaxy-user] genome for Stenotrophomans
Hello Ateequr, The quickest way to use new genomes with tools is to use them as a custom reference genome. To do this, load the genome in fasta format into your history and set tool form options to use reference genomes from the history. Best practices: 1 - double check that the format is strict fasta (all lines wrapped to same length, no extra lines or hidden characters, sequence entries are unique within file). 2 - use the same genome dataset for all steps within an analysis 3 - load using FTP and make certain load is complete http://galaxyproject.org/wiki/Learn/Upload%20via%20FTP Hopefully this helps! Best, Jen Galaxy team On 1/13/12 7:00 AM, Ateequr Rehman wrote: Dear Galaxy Administrator I am analysing transcriptome and genome of clinical isolatesStenotrophomonasmaltophilia, would be highly obliged if you could please upload Stenotrophomonas maltophilia K279 and Stenotrophomonas maltophilia R551-3 genome acccesion numbers at NCBI are as following Stenotrophomonas maltophilia K279 (Accession AM743169) *Stenotrophomonas maltophilia R551-3*, complete genome http://www.ncbi.nlm.nih.gov/nuccore/CP00.1 Accession: CP00 Thanking you all in advance Ateequr Rehman ___ 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/
Re: [galaxy-user] Unable to download files from barcode splitter (from public Galaxy)
Hello Alicia, Would you please share with me the history on the public Main server that you are having trouble downloading the data from? Use Options - Share or Publish, generate the link or add my email as a shared user, and email the link or name of the history back to me directly. Thanks, Jen Galaxy team On 1/13/12 1:28 AM, Poh Leng Chong wrote: Hi, I run Barcode Splitter (from public Galaxy server) and am unable to download the text files generated by the barcode splitter, got an error message which says ' Could not find 'FASTQ_Groomer_on_data_1__V1.txt' on the extra files path /galaxy/main_pool/pool2/files/003/610/dataset_3610002_files/FASTQ_Groomer_on_data_1__V1.txt. The run was Ok (green colour) but yet i was unable to download the text files. Could you please advise? Also, I wonder if you could help regarding the local Galaxy.. I used VirtualBox to install the local copy, and installed according to the instructions as in the website, command as hg clone https://; The setup was smooth and went OK. The problem starts when I run the local Galaxy using real data. I could upload the files, but have problems with the fastQC and barcode splitter, I could not proceed any further since these two operations could not be run...The error messages are: FastQC An error occurred running this job: Traceback (most recent call last): File /home/Desktop/galaxy-dist/tools/rgenetics/rgFastQC.py, line 141, inmodule assert os.path.isfile(opts.executable),'##rgFastQC.py error - cannot find executable %s' % opts.executable AssertionError Barcode Splitter An error occurred running this job: /home/Desktop/galaxy-dist/tools/fastx_toolkit/fastx_barcode_splitter_galaxy_wrapper.sh: line 65: fastx_barcode_splitter.pl: command not found gzip: stdout: Broken pipe Can anyone help me please? I installed the local Galaxy but could not proceed further. I then used the public Galaxy but could not download the files Hope to hear from you. Thanks very much. Best regards Alicia ___ 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/
