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_desai@persistent.co.in<mailto:aarti_desai@persistent.co.in> | Cell: +91-9673009492 | Tel: + 91-20-67036348 Persistent Systems Ltd. | Partners in Innovation | www.persistentsys.com<http://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.
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
Thanks a lot. I will try that. Aarti Sent from Samsung mobile Luciano Cosme <cosme.simple@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.
Thanks. Will try that and get back. Sent from Samsung mobile Luciano Cosme <cosme.simple@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.
Hello Luciano, The problem is resolved by using the chmod command below. Thanks a lot. Aarti From: Luciano Cosme [mailto:cosme.simple@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.
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Aarti Desai -
Luciano Cosme