Re: [galaxy-dev] (no subject)
Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail. Thanks in advance
As I wrote in my previous e-mail: "Please send all follow-up with a cc to the mailing list ("reply-all")." In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote:
Hi, Sorry for delayed reply. When I execute "macs_wrapper.py" on command line, I get the following error. python macs_wrapper.py File "<stdin>", line 1 python macs_wrapper.py Thanks in advance
On 01/10/2012 06:31 AM, Vidya .H.K wrote:
Hi, I think macs is exceutable with galaxy user. what happens if you execute "macs_wrapper.py" on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list ("reply-all").
On 01/09/2012 05:04 AM, Vidya .H.K wrote:
Hi, I am new user to galaxy. I have installed galaxy on the Linux local server for ChIP-seq analysis. While running MACS, an error is flagged "An error occurred running this job: /bin/sh: macs: not found" . I have set the path for macs in /bin. But still the error persists. It would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans Thanks in advance. Regards vidya ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
On 01/24/2012 06:19 AM, Vidya .H.K wrote:
Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail.
by simulating a complete command line I meant the following: You look how "macs_wrapper.py" is called by galaxy. This is written in the "macs_wrapper.xml" and then you execute the same command line. But I just realize, you have re-submitted the same question in a different e-mail thread again (unfortunately, again without a subject line).....
Thanks in advance
As I wrote in my previous e-mail: "Please send all follow-up with a cc to the mailing list ("reply-all")." In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote:
Hi, Sorry for delayed reply. When I execute "macs_wrapper.py" on command line, I get the following error. python macs_wrapper.py File "<stdin>", line 1 python macs_wrapper.py Thanks in advance
On 01/10/2012 06:31 AM, Vidya .H.K wrote:
Hi, I think macs is exceutable with galaxy user. what happens if you execute "macs_wrapper.py" on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list ("reply-all").
On 01/09/2012 05:04 AM, Vidya .H.K wrote: > Hi, > I am new user to galaxy. I have installed galaxy on the Linux local server > for ChIP-seq analysis. While running MACS, an error is flagged > "An error occurred running this job: /bin/sh: macs: not found" . > I have set the path for macs in /bin. But still the error persists. It > would be great if any one help me resolve this problem. Hi Vidya Is macs executable for the galaxy user (ie the user the galaxy server is running as) ? Regards, Hans > Thanks in advance. > Regards > vidya > ___________________________________________________________ Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/
Hi Vidya, One quick thing to check is that you installed MACS version 1.3 which is supported by the wrapper and not version 1.4 which is not yet supported. Thanks for using Galaxy, Dan On Jan 24, 2012, at 7:41 AM, Hans-Rudolf Hotz wrote:
On 01/24/2012 06:19 AM, Vidya .H.K wrote:
Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail.
by simulating a complete command line I meant the following:
You look how "macs_wrapper.py" is called by galaxy. This is written in the "macs_wrapper.xml" and then you execute the same command line.
But I just realize, you have re-submitted the same question in a different e-mail thread again (unfortunately, again without a subject line).....
Thanks in advance
As I wrote in my previous e-mail: "Please send all follow-up with a cc to the mailing list ("reply-all")." In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote:
Hi, Sorry for delayed reply. When I execute "macs_wrapper.py" on command line, I get the following error. python macs_wrapper.py File "<stdin>", line 1 python macs_wrapper.py Thanks in advance
On 01/10/2012 06:31 AM, Vidya .H.K wrote:
Hi, I think macs is exceutable with galaxy user. what happens if you execute "macs_wrapper.py" on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list ("reply-all"). > On 01/09/2012 05:04 AM, Vidya .H.K wrote: >> Hi, >> I am new user to galaxy. I have installed galaxy on the Linux local server >> for ChIP-seq analysis. While running MACS, an error is flagged >> "An error occurred running this job: /bin/sh: macs: not found" . >> I have set the path for macs in /bin. But still the error persists. It >> would be great if any one help me resolve this problem. > Hi Vidya > Is macs executable for the galaxy user (ie the user the galaxy server > is > running as) ? > Regards, Hans >> Thanks in advance. >> Regards >> vidya >> ___________________________________________________________ Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi Dan, Thank you Dan. This was very helpful.I installed MACS version 1.3 and now the tool is working.
Hi Vidya,
One quick thing to check is that you installed MACS version 1.3 which is supported by the wrapper and not version 1.4 which is not yet supported.
Thanks for using Galaxy,
Dan
On Jan 24, 2012, at 7:41 AM, Hans-Rudolf Hotz wrote:
On 01/24/2012 06:19 AM, Vidya .H.K wrote:
Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail.
by simulating a complete command line I meant the following:
You look how "macs_wrapper.py" is called by galaxy. This is written in the "macs_wrapper.xml" and then you execute the same command line.
But I just realize, you have re-submitted the same question in a different e-mail thread again (unfortunately, again without a subject line).....
Thanks in advance
As I wrote in my previous e-mail: "Please send all follow-up with a cc to the mailing list ("reply-all")." In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote:
Hi, Sorry for delayed reply. When I execute "macs_wrapper.py" on command line, I get the following error. python macs_wrapper.py File "<stdin>", line 1 python macs_wrapper.py Thanks in advance
On 01/10/2012 06:31 AM, Vidya .H.K wrote: > Hi, > I think macs is exceutable with galaxy user. what happens if you execute "macs_wrapper.py" on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list ("reply-all"). >> On 01/09/2012 05:04 AM, Vidya .H.K wrote: >>> Hi, >>> I am new user to galaxy. I have installed galaxy on the Linux >>> local server >>> for ChIP-seq analysis. While running MACS, an error is flagged >>> "An error occurred running this job: /bin/sh: macs: not >>> found" . >>> I have set the path for macs in /bin. But still the error >>> persists. It >>> would be great if any one help me resolve this problem. >> Hi Vidya >> Is macs executable for the galaxy user (ie the user the galaxy server >> is >> running as) ? >> Regards, Hans >>> Thanks in advance. >>> Regards >>> vidya >>> ___________________________________________________________ >>> Please keep all replies on the list by using "reply all" >>> in your mail client. To manage your subscriptions to this >>> and other Galaxy lists, please use the interface at: >>> http://lists.bx.psu.edu/ >
___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at:
Hi, Thank you very much for your help. I have resolved the problem. I had install MACS version 1.3 instead of MACS version 1.4. Now the tool is working fine.
On 01/24/2012 06:19 AM, Vidya .H.K wrote:
Hi, Actually I am not computer expert as well. I have just started to work in this area. so I am not able to figure out how to solve this problem. I request you to elaborate on what you meant in your previous mail.
by simulating a complete command line I meant the following:
You look how "macs_wrapper.py" is called by galaxy. This is written in the "macs_wrapper.xml" and then you execute the same command line.
But I just realize, you have re-submitted the same question in a different e-mail thread again (unfortunately, again without a subject line).....
Thanks in advance
As I wrote in my previous e-mail: "Please send all follow-up with a cc to the mailing list ("reply-all")." In order to debug you situation you need to simulate a complete commandline, the same Galaxy is doing. Regards, Hans On 01/23/2012 05:35 AM, Vidya .H.K wrote:
Hi, Sorry for delayed reply. When I execute "macs_wrapper.py" on command line, I get the following error. python macs_wrapper.py File "<stdin>", line 1 python macs_wrapper.py Thanks in advance
On 01/10/2012 06:31 AM, Vidya .H.K wrote:
Hi, I think macs is exceutable with galaxy user. what happens if you execute "macs_wrapper.py" on the command line? Regards, Hans PS: Please send all follow-up with a cc to the mailing list ("reply-all"). > On 01/09/2012 05:04 AM, Vidya .H.K wrote: >> Hi, >> I am new user to galaxy. I have installed galaxy on the Linux >> local server >> for ChIP-seq analysis. While running MACS, an error is flagged >> "An error occurred running this job: /bin/sh: macs: not >> found" . >> I have set the path for macs in /bin. But still the error >> persists. It >> would be great if any one help me resolve this problem. > Hi Vidya > Is macs executable for the galaxy user (ie the user the galaxy server > is > running as) ? > Regards, Hans >> Thanks in advance. >> Regards >> vidya >> ___________________________________________________________ Please keep all replies on the list by using "reply all" >> in your mail client. To manage your subscriptions to this >> and other Galaxy lists, please use the interface at: >> http://lists.bx.psu.edu/
participants (3)
-
Daniel Blankenberg -
Hans-Rudolf Hotz -
Vidya .H.K