Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: zhengqiu cai caizhq2...@yahoo.com.cn 抄送: Jennifer Jackson j...@bx.psu.edu, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午5:18 Ah. Then you probably have a library path problem. Here's how we do

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

that SGE knows the path of samtools. Cai --- 12年4月18日，周三, Ross ross.laza...@gmail.com 写道： 发件人: Ross ross.laza...@gmail.com 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: zhengqiu cai caizhq2...@yahoo.com.cn 抄送: Jennifer Jackson j...@bx.psu.edu

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

libraries? Thank you, Cai --- 12年4月18日，周三, Ross ross.laza...@gmail.com 写道： 发件人: Ross ross.laza...@gmail.com 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: zhengqiu cai caizhq2...@yahoo.com.cn 抄送: Jennifer Jackson j...@bx.psu.edu, galaxy-dev

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

' fully functional for the cluster(it is on the local machine)? or should I set some other libraries? Thank you, Cai --- 12年4月18日，周三, Ross ross.laza...@gmail.com 写道： 发件人: Ross ross.laza...@gmail.com 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

--- 12年4月18日，周三, Ross ross.laza...@gmail.com 写道： 发件人: Ross ross.laza...@gmail.com 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: zhengqiu cai caizhq2...@yahoo.com.cn 抄送: Jennifer Jackson j...@bx.psu.edu, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

Hi Cai, Please double check that your env.sh file contains the following: PATH=/mnt/galaxyTools/tools/samtools/0.1.12:$PATH export PATH http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies Hopefully this helps, Jen Galaxy team On 4/16/12 12:43 PM, zhengqiu cai wrote: Hi

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

the tool path) Thanks you very much, Cai --- 12年4月18日，周三, Jennifer Jackson j...@bx.psu.edu 写道： 发件人: Jennifer Jackson j...@bx.psu.edu 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: zhengqiu cai caizhq2...@yahoo.com.cn 抄送: galaxy-dev@lists.bx.psu.edu

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

for since it does not work across the cluster. Cai --- 12年4月18日，周三, Ross ross.laza...@gmail.com 写道： 发件人: Ross ross.laza...@gmail.com 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: zhengqiu cai caizhq2...@yahoo.com.cn 抄送: Jennifer Jackson j

Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

ross.laza...@gmail.com 写道： 发件人: Ross ross.laza...@gmail.com 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found 收件人: zhengqiu cai caizhq2...@yahoo.com.cn 抄送: Jennifer Jackson j...@bx.psu.edu, galaxy-dev@lists.bx.psu.edu 日期: 2012年4月18日,周三,上午4:59 Cai - if you

[galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh: samtools: not found

Hi All, I was trying to setup the Galaxy tool dependencies, and I met the following problem when running sam-to-bam in samtools: Traceback (most recent call last): File /mnt/galaxyTools/cai_galaxy-dist/lib/galaxy/jobs/runners/drmaa.py, line 336, in finish_job