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.inmailto:aarti_desai@persistent.co.in | Cell: +91-9673009492 | Tel: + 91-20-67036348 Persistent Systems Ltd. | Partners in Innovation | www.persistentsys.comhttp://www.persistentsys.com/
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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
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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
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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
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galaxy-user@lists.galaxyproject.org
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Aarti Desai -
Luciano Cosme