Re: [galaxy-user] Problem with ftp transfer of large bam files
Hi again, The problem with ftp transferred files not showing up under my account in Galaxy (main) is actually solved now. I could be an issue of being logged in from many clients at the same time - when I logout from Galaxy and then start ftp transfer - upon logging in to Galaxy again I can indeed see the files listed under Upload File. All your items 1-4 below checked out as ok by the way and I was below the quota. Cheers /Hans From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: den 4 juli 2012 22:39 To: Hans Matsson Cc: galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] Problem with ftp transfer of large bam files Helllo Hans, Some items to double check: 1 - The ftp server is: main.g2.bx.psu.edu 2 - Files are 50G or smaller. This is a hard limit - if your data is larger, a local or cloud instance will be needed: http://getgalaxy.org 3 - FileZilla reports that FTP is successful (there is a tab at the bottom of the UI, click on this and it will list the actual status of transfer, so that there is no ambiguity) 4 - The user/pass credentials used in Filezilla are the same as those being used for your Galaxy account. If you have multiple accounts (you shouldn't...), the data may be in another account. *note:* If you are using multiple accounts, please copy all data to a single account and permanently delete from the others. The public instance supports one account per user only. If you are over quota (have more than 250G of data), this will prevent moving a data file from the FTP transfer area into a history, but it will not block the FTP transfer itself. It does sound as if you have already seen the FTP wiki/screencast, but I'll post the wiki just in case: http://wiki.g2.bx.psu.edu/FTPUpload Hopefully one of these helps to work out the issue, Jen Galaxy team On 7/4/12 7:24 AM, Hans Matsson wrote: Hi, I´m using Galaxy (main) browser on a Win 7 PC to get statistics from my sequencing runs. Now I have bam files which are too big for upload from my local hard drive so I tried to ftp upload to main.g2.bx.psu.edu via a client (FileZilla). The transfer of files seems to be complete but the files do not appear under Get Data/Upload File and I have the message Your FTP upload directory contains no files. I have tried to upload txt, zip, and bam files by ftp but nothing worked. Any suggestions? Many thanks /Hans Hans Matsson, PhD Karolinska Institutet Department of Biosciences and Nutrition Novum Hälsovägen 7-9 SE-141 83 Huddinge, Sweden Email: hans.mats...@ki.semailto:hans.mats...@ki.se Phone (office): +46-8-524 81143 ¤¤ ___ 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://galaxyproject.org ___ 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] Data from history now showing up in fastq drop down
Hi All, We have a galaxy local install. Thanks to Carlos's suggestion, I was able to get the reference genome index to show up in the interface. Now, I am trying to get the data into the galaxy system. I have followed the instructions in the link below to create data libraries. http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Libraries I have modified the following sections in the universe_wsgi.ini file: # Add an option to the library upload form which allows administrators to # upload a directory of files. library_import_dir = /media/FreeAgent GoFlex Drive_/HDD1/Project # Add an option to the admin library upload tool allowing admins to paste # filesystem paths to files and directories in a box, and these paths will be # added to a library. Set to True to enable. Please note the security # implication that this will give Galaxy Admins access to anything your Galaxy # user has access to. allow_library_path_paste = True I created a data library and using the Add dataset function, I pasted the path of my data directory in the galaxy UI and selected the link to files without copying into galaxy option. This picked up all the files that were present in the directory and except for a couple of files, the job seems to have completed successfully. Now I am not sure how to actually analyze this data. I performed the Import to current history operation on two paired end fastq files I want to analyze. These show up in the history with the appropriate size. But when I choose the Map with BWA for Illumina option, the two fastq files do not show up in the FASTQ file drop down. These files do show up in the list of files for running fastqc I have also restarted the server after importing the data in the history, but the problem persists. Any input on how to go about analyzing the data in the local galaxy instance once it has been brought into the galaxy frame work is highly appreciated. Thanks for the help. Regards, Aarti Aarti Desai, Ph.D | Domain Specialist - Life Sciences aarti_de...@persistent.co.inmailto:aarti_de...@persistent.co.in | Cell: +91-9673009492 | Tel: + 91-20-67036348 Persistent Systems Ltd. | Partners in Innovation | www.persistentsys.comhttp://www.persistentsys.com/ DISCLAIMER == This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. ___ 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] Permission denied error when running fastqc
Hello All, One more problem when running analysis on local galaxy install. I am trying to run fastqc on a fastq file I just imported. I have fastqc in ~/Programs/Galaxy/galaxy-dist/tool-data/shared/jars/FastQC I am getting the following error ## odpath=None: No output found in None. Output for the run was: /bin/sh: /root/Programs/Galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc: Permission denied My guess is the output directory path is not set. If my guess is correct, the question is where do I set the path? If my guess is wrong, any help interpreting the error greatly appreciated. Aarti Aarti Desai, Ph.D | Domain Specialist - Life Sciences aarti_de...@persistent.co.inmailto:aarti_de...@persistent.co.in | Cell: +91-9673009492 | Tel: + 91-20-67036348 Persistent Systems Ltd. | Partners in Innovation | www.persistentsys.comhttp://www.persistentsys.com/ DISCLAIMER == This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. ___ 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] Data from history now showing up in fastq drop down
Hi, I believe you have to run Fastq Groomer first to convert it to sanger format. Then you will be able to see your dataset. https://main.g2.bx.psu.edu/u/dan/p/fastq Best, Luciano ___ 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] Permission denied error when running fastqc
Hi, You will have to change the permission of fastqc to be executable. You can open your terminal, log as root and change it. Open your terminal, type sudo su, then it will ask your password. After you enter your password type chmod 777 /root/Programs/Galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc Best, Luciano ___ 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] Permission denied error when running fastqc
Thanks a lot. I will try that. Aarti Sent from Samsung mobile Luciano Cosme cosme.sim...@gmail.com wrote: Hi, You will have to change the permission of fastqc to be executable. You can open your terminal, log as root and change it. Open your terminal, type sudo su, then it will ask your password. After you enter your password type chmod 777 /root/Programs/Galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc Best, Luciano DISCLAIMER == This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. ___ 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] Permission denied error when running fastqc
Thanks. Will try that and get back. Sent from Samsung mobile Luciano Cosme cosme.sim...@gmail.com wrote: Hi, You will have to change the permission of fastqc to be executable. You can open your terminal, log as root and change it. Open your terminal, type sudo su, then it will ask your password. After you enter your password type chmod 777 /root/Programs/Galaxy/galaxy-dist/tool-data/shared/jars/FastQC/fastqc Best, Luciano DISCLAIMER == This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. ___ 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] Data from history now showing up in fastq drop down
Thanks. Sent from Samsung mobile Luciano Cosme cosme.sim...@gmail.com wrote: Hi, I believe you have to run Fastq Groomer first to convert it to sanger format. Then you will be able to see your dataset. https://main.g2.bx.psu.edu/u/dan/p/fastq Best, Luciano DISCLAIMER == This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. ___ 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/
