Re: [galaxy-user] Permission denied error when running fastqc
Hello Luciano, The problem is resolved by using the chmod command below. Thanks a lot. Aarti From: Luciano Cosme [mailto:cosme.sim...@gmail.com] Sent: Friday, July 06, 2012 9:58 PM To: Aarti Desai Cc: galaxy-user@lists.bx.psu.edu Subject: 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 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] 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] 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/
Re: [galaxy-user] Getting reference index files in local galaxy install
Hello Carlos, Thanks a lot for the tip. The tab trick has fixed the problem. Regards, Aarti -Original Message- From: Carlos Borroto [mailto:carlos.borr...@gmail.com] Sent: Thursday, July 05, 2012 9:12 PM To: Avik Datta Cc: Aarti Desai; galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Getting reference index files in local galaxy install Also make sure you are using TABs to separate the fields in the .loc file, this has bitten me several time in the past. My vim config places 4 spaces instead of TAB, to deactivate this option you can do :set noexpandtab. Hope it helps, Carlos On Thu, Jul 5, 2012 at 4:39 AM, Avik Datta reach4a...@gmail.com wrote: Hi Aarti, Check the name of your ref file. If it is hg19.fa, then modify loc file as hg19 hg19 HG19_BWA /root/Ref_INDEX/HG19BWAIndex/base/hg19.fa Avik Datta On Thu, Jul 5, 2012 at 1:42 PM, Aarti Desai aarti_de...@persistent.co.in wrote: Hi, We have a local install of galaxy and I’m trying to add the reference index files for bwa using the information provided in the following link http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup I have modified the bwa_index.loc file present in the ../tool-data directory by adding the path to where the index is on our server (Also attached). However, even after restarting the server, the reference genome does not show when choosing the “use a built-in index option”. I’m not sure whether the loc file is correctly created and whether any other configuration file needs to be changed/updated. Help in the matter greatly appreciated. Thanks, Aarti From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Jennifer Jackson Sent: Thursday, July 05, 2012 1:23 AM To: Lindsey Kelly Cc: galaxy-user@lists.bx.psu.edu Subject: Re: [galaxy-user] Initial QC and grooming for Illumina HiSeq2000 paired end RNAseq data Hello Lindsey, Yes, you have this correct. The general path would be to: - join forward and reverse data per run - run FASTQ Groomer FastQC (note: if your data is already in Sanger FASTQ format with Phred+33 quality scaled values, the datatype '.fastqsanger' can be directly assigned and the FASTQ Groomer step skipped. This is likely true if your data is a from the latest CASAVA pipeline, but please double check.) - discard data as needed based on quality - split forward and reverse data that passes QC - concatenate all forward reads from a sample into one FASTQ file - concatenate all reverse reads from a sample into one FASTQ file. - for each sample, run TopHat using the two concatenated FASTQ files To manipulate paired end data, please see the tools - NGS: QC and manipulation: FASTQ splitter FASTQ joiner. To combined data files head-to-tail from multiple runs into a single FASTQ file please see the tool - Text Manipulation: Concatenate datasets. I am not sure of the actual volume of data, but if these start to get large or TopHat errors with a memory problem, a local or cluster instance would be the recommendation: http://getgalaxy.org For reference: http://tophat.cbcb.umd.edu/manual.html http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html Hopefully this helps. Others are welcome to post comments/suggestions. Jen Galaxy team On 7/2/12 11:17 AM, Lindsey Kelly wrote: I am trying to do RNAseq analysis on Paired end data from the Hiseq2000. I have about 50 files for each sample (25 forward and 25 reverse - although each sample has a different number of files). I think that I need to: -convert them into FASTQ sanger format using the FASTSQ groomer tool -check the quality using the FASTQqc tool I don't know how to handle this many files. Do I have to groom and run the QC for each file? Should I join the paired files and run both tools on each pair, or should I combine all of the data for each sample (which I don't know how to do) and then groom and run the QC for all of the reads for the sample. Thanks in advance for advice Lindsey ___ 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 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
[galaxy-user] Training on NGS data analysis
Hi Jennifer, We are working on developing NGS data analysis pipeline. Does your institution have a training program where one or two people from my team can be trained on NGS data analysis, particularly de novo genome assembly? Regards, Aarti Dr. Aarti Desai | Domain Specialist - Life Sciences Domain aarti_de...@persistent.co.inmailto:aarti_de...@persistent.co.in | Cell: +91-9673009492 | Tel: +91-20-30236348 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/
