--- 12年4月18日，周三, Ross 写道：
> 发件人: Ross
> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh:
> samtools: not found
> 收件人: "zhengqiu cai"
> 抄送: "Jennifer Jackson" , galaxy-dev@lists.bx.psu.edu
> 日期: 2012年4月18日,周三,下午11:46
> Hi, Cai.
> A
xecutable 'samtools' 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 写道：
>
>> 发件人: Ross
>> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata
uld I set some other libraries?
Thank you,
Cai
--- 12年4月18日，周三, Ross 写道：
> 发件人: Ross
> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh:
> samtools: not found
> 收件人: "zhengqiu cai"
> 抄送: "Jennifer Jackson" , galaxy-dev@lists.bx.psu.edu
>
dx.pl $input1 $output1
>
>
>
>
>
>
>
>
>
> It works, which shows that SGE knows the path of samtools.
>
>
> Cai
>
> --- 12年4月18日，周三, Ross 写道：
>
>> 发件人: Ross
>> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/s
creates fasta index
samtools_faidx.pl $input1 $output1
It works, which shows that SGE knows the path of samtools.
Cai
--- 12年4月18日，周三, Ross 写道：
> 发件人: Ross
> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh:
> samtools: not
t;
>
> Cai
>
> --- 12年4月18日，周三, Ross 写道：
>
>> 发件人: Ross
>> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh:
>> samtools: not found
>> 收件人: "zhengqiu cai"
>> 抄送: "Jennifer Jackson" , galaxy-dev@lists.bx.psu.edu
a solution for
since it does not work across the cluster.
Cai
--- 12年4月18日，周三, Ross 写道：
> 发件人: Ross
> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh:
> samtools: not found
> 收件人: "zhengqiu cai"
> 抄送: "Jennifer Jackson" , galaxy-de
wa and bowtie worked well using the same
> setting method(put env.sh in the tools directory to set the tool path)
>
>
> Thanks you very much,
>
> Cai
> --- 12年4月18日，周三, Jennifer Jackson 写道：
>
>> 发件人: Jennifer Jackson
>> 主题: Re: [galaxy-dev] Excepti
setting method(put env.sh in the tools directory to set the tool path)
Thanks you very much,
Cai
--- 12年4月18日，周三, Jennifer Jackson 写道：
> 发件人: Jennifer Jackson
> 主题: Re: [galaxy-dev] Exception: Error Setting BAM Metadata: /bin/sh:
> samtools: not found
> 收件人: "zhengqiu cai&q
Hi Cai,
Please double check that your env.sh file contains the following:
PATH="/mnt/galaxyTools/tools/samtools/0.1.12:$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 A
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
drm_job_state.job_wrapper.fi
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