macs error for chipseq data
Hi Kathryn, I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility. Thanks! Jen Galaxy team On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
Hi Jen,
Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out.
It seems to me that MACS was installed.... What is the issue?
Thank you very much,
Kathryn
On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much,
Kathryn
**
*From:*Jennifer Jackson [mailto:jen@bx.psu.edu] *Sent:* Friday, January 11, 2013 3:48 AM *To:* Sun, Wenping [USA] *Cc:* galaxy-user@bx.psu.edu *Subject:* [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to the galaxy-dev@bx.psu.edu <mailto:galaxy-dev@bx.psu.edu> mailing list would be best,
Thanks!
Jen Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:
Dear galaxy users,
I've encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error
An error occurred running this job: //bin/sh: macs: not found/
//
Anybody can kindly provide some hints?
Thanks,
Kathryn
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
There's an issue with the MACS installation on the current cloud tools volume (which will be fixed with the next volume update coming soon). For existing instances, you can get MACS working correctly by executing the following two commands (which change the default version of macs used) after ssh'ing in to your instance: sudo su galaxy ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 /mnt/galaxyTools/tools/macs/default And that's it, no need to restart galaxy or anything. -Dannon On Jan 11, 2013, at 10:59 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility.
Thanks! Jen Galaxy team
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
Hi Jen,
Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out.
It seems to me that MACS was installed…. What is the issue?
Thank you very much, Kathryn On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much, Kathryn
From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-user@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to the galaxy-dev@bx.psu.edu mailing list would be best,
Thanks!
Jen Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users,
I’ve encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error
An error occurred running this job: /bin/sh: macs: not found
Anybody can kindly provide some hints?
Thanks, Kathryn
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
-- Jennifer Hillman-Jackson Galaxy Support and Training
I linked the macs version 1.3.7.1 to the default as the commands below. It runs, however, still get the error message as below -- MACS on data 65 and data 66 (peaks: bed) 0 bytes An error occurred running this job: INFO @ Fri, 11 Jan 2013 19:30:50: # ARGUMENTS LIST: # name = MACS_in_Galaxy # format = SAM # ChIP-seq file = /mnt/galaxyData/files/000/dataset_66.dat # control file = /mnt/galaxyData/files/000/dataset_65.dat # effective genome size = 2.70e+09 # tag size I switched to version 1.4.1 and got the error message same as the first time. Thanks again, Kathryn -----Original Message----- From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Friday, January 11, 2013 12:12 PM To: Jennifer Jackson Cc: Galaxy Dev; Sun, Wenping [USA] Subject: [External] Re: macs error for chipseq data There's an issue with the MACS installation on the current cloud tools volume (which will be fixed with the next volume update coming soon). For existing instances, you can get MACS working correctly by executing the following two commands (which change the default version of macs used) after ssh'ing in to your instance: sudo su galaxy ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 /mnt/galaxyTools/tools/macs/default And that's it, no need to restart galaxy or anything. -Dannon On Jan 11, 2013, at 10:59 AM, Jennifer Jackson <jen@bx.psu.edu<mailto:jen@bx.psu.edu>> wrote:
Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility.
Thanks!
Jen
Galaxy team
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
Hi Jen,
Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out.
It seems to me that MACS was installed.... What is the issue?
Thank you very much,
Kathryn
On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much,
Kathryn
From: Jennifer Jackson [mailto:jen@bx.psu.edu]
Sent: Friday, January 11, 2013 3:48 AM
To: Sun, Wenping [USA]
Cc: galaxy-user@bx.psu.edu<mailto:galaxy-user@bx.psu.edu>
Subject: [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis:
http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies
http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here:
https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to
the galaxy-dev@bx.psu.edu<mailto:galaxy-dev@bx.psu.edu> mailing list would be best,
Thanks!
Jen
Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:
Dear galaxy users,
I've encountered the error while running macs on galaxy for chipseq
data. I used fastq groomed files as input and had the following error
An error occurred running this job: /bin/sh: macs: not found
Anybody can kindly provide some hints?
Thanks,
Kathryn
___________________________________________________________
The Galaxy User list should be used for the discussion of Galaxy
analysis and other features on the public server at usegalaxy.org.
Please keep all replies on the list by using "reply all" in your mail
client. For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists, please
use the interface at:
--
Jennifer Hillman-Jackson
Galaxy Support and Training
--
Jennifer Hillman-Jackson
Galaxy Support and Training
1.3.7.1 is definitely the version you want -- the Galaxy wrappers are not yet compatible with 1.4* versions (so they are guaranteed to fail). Is there more error output available, or is that it, ending with #tag size? On Jan 11, 2013, at 4:48 PM, "Sun, Wenping [USA]" <Sun_Wenping@bah.com> wrote:
I linked the macs version 1.3.7.1 to the default as the commands below.
It runs, however, still get the error message as below --
MACS on data 65 and data 66 (peaks: bed) 0 bytes An error occurred running this job: INFO @ Fri, 11 Jan 2013 19:30:50: # ARGUMENTS LIST: # name = MACS_in_Galaxy # format = SAM # ChIP-seq file = /mnt/galaxyData/files/000/dataset_66.dat # control file = /mnt/galaxyData/files/000/dataset_65.dat # effective genome size = 2.70e+09 # tag size
I switched to version 1.4.1 and got the error message same as the first time.
Thanks again, Kathryn
-----Original Message----- From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Friday, January 11, 2013 12:12 PM To: Jennifer Jackson Cc: Galaxy Dev; Sun, Wenping [USA] Subject: [External] Re: macs error for chipseq data
There's an issue with the MACS installation on the current cloud tools volume (which will be fixed with the next volume update coming soon).
For existing instances, you can get MACS working correctly by executing the following two commands (which change the default version of macs used) after ssh'ing in to your instance:
sudo su galaxy ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 /mnt/galaxyTools/tools/macs/default
And that's it, no need to restart galaxy or anything.
-Dannon
On Jan 11, 2013, at 10:59 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility.
Thanks! Jen Galaxy team
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
Hi Jen,
Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out.
It seems to me that MACS was installed…. What is the issue?
Thank you very much, Kathryn On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much, Kathryn
From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-user@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to the galaxy-dev@bx.psu.edu mailing list would be best,
Thanks!
Jen Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users,
I’ve encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error
An error occurred running this job: /bin/sh: macs: not found
Anybody can kindly provide some hints?
Thanks, Kathryn
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
-- Jennifer Hillman-Jackson Galaxy Support and Training
For the output of 1.3.7.1, I didn't check wiggle files since it takes longer time. So the output are bed and html report, both with the same error and that's all I have from the right panel below the file names. I already deleted those errored-outputs. Thanks, Kathryn -----Original Message----- From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Friday, January 11, 2013 4:56 PM To: Sun, Wenping [USA] Cc: Jennifer Jackson; Galaxy Dev Subject: Re: [External] Re: macs error for chipseq data 1.3.7.1 is definitely the version you want -- the Galaxy wrappers are not yet compatible with 1.4* versions (so they are guaranteed to fail). Is there more error output available, or is that it, ending with #tag size? On Jan 11, 2013, at 4:48 PM, "Sun, Wenping [USA]" <Sun_Wenping@bah.com> wrote:
I linked the macs version 1.3.7.1 to the default as the commands below.
It runs, however, still get the error message as below --
MACS on data 65 and data 66 (peaks: bed) 0 bytes An error occurred running this job: INFO @ Fri, 11 Jan 2013 19:30:50: # ARGUMENTS LIST: # name = MACS_in_Galaxy # format = SAM # ChIP-seq file = /mnt/galaxyData/files/000/dataset_66.dat # control file = /mnt/galaxyData/files/000/dataset_65.dat # effective genome size = 2.70e+09 # tag size
I switched to version 1.4.1 and got the error message same as the first time.
Thanks again, Kathryn
-----Original Message----- From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Friday, January 11, 2013 12:12 PM To: Jennifer Jackson Cc: Galaxy Dev; Sun, Wenping [USA] Subject: [External] Re: macs error for chipseq data
There's an issue with the MACS installation on the current cloud tools volume (which will be fixed with the next volume update coming soon).
For existing instances, you can get MACS working correctly by executing the following two commands (which change the default version of macs used) after ssh'ing in to your instance:
sudo su galaxy ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 /mnt/galaxyTools/tools/macs/default
And that's it, no need to restart galaxy or anything.
-Dannon
On Jan 11, 2013, at 10:59 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility.
Thanks! Jen Galaxy team
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
Hi Jen,
Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out.
It seems to me that MACS was installed.... What is the issue?
Thank you very much, Kathryn On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much, Kathryn
From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-user@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to the galaxy-dev@bx.psu.edu mailing list would be best,
Thanks!
Jen Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users,
I've encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error
An error occurred running this job: /bin/sh: macs: not found
Anybody can kindly provide some hints?
Thanks, Kathryn
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
-- Jennifer Hillman-Jackson Galaxy Support and Training
The error is most likely caused by your input data and parameter choices. If you click the little bug icon in the history for a dataset in the error state, you'll see the full error output display that will have more information and will hopefully help you figure out what's going on. One potential problem might be that your MFOLD is too high, but we'd need to see the full error report to determine that. On Jan 11, 2013, at 5:01 PM, "Sun, Wenping [USA]" <Sun_Wenping@bah.com> wrote:
For the output of 1.3.7.1, I didn't check wiggle files since it takes longer time. So the output are bed and html report, both with the same error and that's all I have from the right panel below the file names. I already deleted those errored-outputs.
Thanks, Kathryn
-----Original Message----- From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Friday, January 11, 2013 4:56 PM To: Sun, Wenping [USA] Cc: Jennifer Jackson; Galaxy Dev Subject: Re: [External] Re: macs error for chipseq data
1.3.7.1 is definitely the version you want -- the Galaxy wrappers are not yet compatible with 1.4* versions (so they are guaranteed to fail). Is there more error output available, or is that it, ending with #tag size?
On Jan 11, 2013, at 4:48 PM, "Sun, Wenping [USA]" <Sun_Wenping@bah.com> wrote:
I linked the macs version 1.3.7.1 to the default as the commands below.
It runs, however, still get the error message as below --
MACS on data 65 and data 66 (peaks: bed) 0 bytes An error occurred running this job: INFO @ Fri, 11 Jan 2013 19:30:50: # ARGUMENTS LIST: # name = MACS_in_Galaxy # format = SAM # ChIP-seq file = /mnt/galaxyData/files/000/dataset_66.dat # control file = /mnt/galaxyData/files/000/dataset_65.dat # effective genome size = 2.70e+09 # tag size
I switched to version 1.4.1 and got the error message same as the first time.
Thanks again, Kathryn
-----Original Message----- From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Friday, January 11, 2013 12:12 PM To: Jennifer Jackson Cc: Galaxy Dev; Sun, Wenping [USA] Subject: [External] Re: macs error for chipseq data
There's an issue with the MACS installation on the current cloud tools volume (which will be fixed with the next volume update coming soon).
For existing instances, you can get MACS working correctly by executing the following two commands (which change the default version of macs used) after ssh'ing in to your instance:
sudo su galaxy ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 /mnt/galaxyTools/tools/macs/default
And that's it, no need to restart galaxy or anything.
-Dannon
On Jan 11, 2013, at 10:59 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility.
Thanks! Jen Galaxy team
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
Hi Jen,
Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out.
It seems to me that MACS was installed.... What is the issue?
Thank you very much, Kathryn On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much, Kathryn
From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-user@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to the galaxy-dev@bx.psu.edu mailing list would be best,
Thanks!
Jen Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users,
I've encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error
An error occurred running this job: /bin/sh: macs: not found
Anybody can kindly provide some hints?
Thanks, Kathryn
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
-- Jennifer Hillman-Jackson Galaxy Support and Training
Hello, When I sudo galaxy user at ssh terminal, the password prompted for galaxy. What is it? Thanks, Kathryn -----Original Message----- From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Friday, January 11, 2013 12:12 PM To: Jennifer Jackson Cc: Galaxy Dev; Sun, Wenping [USA] Subject: [External] Re: macs error for chipseq data There's an issue with the MACS installation on the current cloud tools volume (which will be fixed with the next volume update coming soon). For existing instances, you can get MACS working correctly by executing the following two commands (which change the default version of macs used) after ssh'ing in to your instance: sudo su galaxy ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1 /mnt/galaxyTools/tools/macs/default And that's it, no need to restart galaxy or anything. -Dannon On Jan 11, 2013, at 10:59 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility.
Thanks! Jen Galaxy team
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
Hi Jen,
Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out.
It seems to me that MACS was installed.... What is the issue?
Thank you very much, Kathryn On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote: Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much, Kathryn
From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-user@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to the galaxy-dev@bx.psu.edu mailing list would be best,
Thanks!
Jen Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users,
I've encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error
An error occurred running this job: /bin/sh: macs: not found
Anybody can kindly provide some hints?
Thanks, Kathryn
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
-- Jennifer Hillman-Jackson Galaxy Support and Training
Are you executing `sudo` as the galaxy user, or as the ubuntu user? The galaxy user is not a sudoer, and you shouldn't need to use sudo for anything you want to do as the galaxy user. The only use in this particular case for using `sudo` as root is to switch *to* the galaxy user. -Dannon On Wed, Feb 27, 2013 at 6:34 PM, Sun, Wenping [USA] <Sun_Wenping@bah.com>wrote:
Hello, When I sudo galaxy user at ssh terminal, the password prompted for galaxy. What is it? Thanks, Kathryn
-----Original Message----- From: Dannon Baker [mailto:dannonbaker@me.com] Sent: Friday, January 11, 2013 12:12 PM To: Jennifer Jackson Cc: Galaxy Dev; Sun, Wenping [USA] Subject: [External] Re: macs error for chipseq data
There's an issue with the MACS installation on the current cloud tools volume (which will be fixed with the next volume update coming soon).
For existing instances, you can get MACS working correctly by executing the following two commands (which change the default version of macs used) after ssh'ing in to your instance:
sudo su galaxy ln -sfn /mnt/galaxyTools/tools/macs/1.3.7.1/mnt/galaxyTools/tools/macs/default
And that's it, no need to restart galaxy or anything.
-Dannon
On Jan 11, 2013, at 10:59 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility.
Thanks! Jen Galaxy team
Hi Jen,
Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote: the right panel and then the error message coming out.
It seems to me that MACS was installed.... What is the issue?
Thank you very much, Kathryn
On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much, Kathryn
From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-user@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to the galaxy-dev@bx.psu.edu mailing list would be best,
Thanks!
Jen Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote: Dear galaxy users,
I've encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error
An error occurred running this job: /bin/sh: macs: not found
Anybody can kindly provide some hints?
Thanks, Kathryn
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists, please use the interface at:
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
-- Jennifer Hillman-Jackson Galaxy Support and Training
Hi Kathryn, We at the modENCODE DCC ( http://www.modencode.org/ ) have been setting up a suite of 3rd party tools for calling peaks ( i.e., macs2, spp, PeakRanger ) using Galaxy on Amazon Cloud the last little while. Please have a look at the README files in the docs folder on our github at https://github.com/modENCODE-DCC/Galaxy Please give it a try and send us your comments/questions to help@modencode.org. Thanks, Q On Fri, Jan 11, 2013 at 10:59 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility.
Thanks! Jen Galaxy team
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
Hi Jen,
Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out.
It seems to me that MACS was installed…. What is the issue?
Thank you very much,
Kathryn
On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much,
Kathryn
From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-user@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to the galaxy-dev@bx.psu.edu mailing list would be best,
Thanks!
Jen Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:
Dear galaxy users,
I’ve encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error
An error occurred running this job: /bin/sh: macs: not found
Anybody can kindly provide some hints?
Thanks,
Kathryn
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
--
Jennifer Hillman-Jackson
Galaxy Support and Training
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
___________________________________________________________ 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:
This is great. For the Galaxy tools, will you be able to submit wrappers to the toolshed? This should make it easier for users to install into their local Galaxy instances. Thanks! -- James Taylor, Assistant Professor, Biology/CS, Emory University On Wed, Jan 16, 2013 at 8:38 AM, Quang Trinh <quang.trinh@gmail.com> wrote:
Hi Kathryn, We at the modENCODE DCC ( http://www.modencode.org/ ) have been setting up a suite of 3rd party tools for calling peaks ( i.e., macs2, spp, PeakRanger ) using Galaxy on Amazon Cloud the last little while. Please have a look at the README files in the docs folder on our github at
https://github.com/modENCODE-DCC/Galaxy
Please give it a try and send us your comments/questions to help@modencode.org.
Thanks,
Q
On Fri, Jan 11, 2013 at 10:59 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility.
Thanks! Jen Galaxy team
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
Hi Jen,
Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out.
It seems to me that MACS was installed…. What is the issue?
Thank you very much,
Kathryn
On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much,
Kathryn
From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-user@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to the galaxy-dev@bx.psu.edu mailing list would be best,
Thanks!
Jen Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:
Dear galaxy users,
I’ve encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error
An error occurred running this job: /bin/sh: macs: not found
Anybody can kindly provide some hints?
Thanks,
Kathryn
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
--
Jennifer Hillman-Jackson
Galaxy Support and Training
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
___________________________________________________________ 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:
___________________________________________________________ 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 James, Yes, we will be putting everything on toolshed shortly. Arthur ( cc'ed ), my student from OICR, will be taking lead on this. Thanks, Q On Wed, Jan 16, 2013 at 11:06 AM, James Taylor <james@jamestaylor.org> wrote:
This is great. For the Galaxy tools, will you be able to submit wrappers to the toolshed? This should make it easier for users to install into their local Galaxy instances. Thanks!
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Wed, Jan 16, 2013 at 8:38 AM, Quang Trinh <quang.trinh@gmail.com> wrote:
Hi Kathryn, We at the modENCODE DCC ( http://www.modencode.org/ ) have been setting up a suite of 3rd party tools for calling peaks ( i.e., macs2, spp, PeakRanger ) using Galaxy on Amazon Cloud the last little while. Please have a look at the README files in the docs folder on our github at
https://github.com/modENCODE-DCC/Galaxy
Please give it a try and send us your comments/questions to help@modencode.org.
Thanks,
Q
On Fri, Jan 11, 2013 at 10:59 AM, Jennifer Jackson <jen@bx.psu.edu> wrote:
Hi Kathryn,
I am going to post this back to the galaxy-dev list and cc Dannon so that he or or one of the developers more experienced with troubleshooting cloud issues can help. My guess is that there is a path problem (covered in the first wiki link) but by no means is that the only possibility.
Thanks! Jen Galaxy team
On 1/11/13 7:38 AM, Sun, Wenping [USA] wrote:
Hi Jen,
Sorry that I missed some part of your email. It is not for local galaxy install. I am using the cloudman from aws and it seemed to have everything for having the input files and reference genome chose. The job was shown on the right panel and then the error message coming out.
It seems to me that MACS was installed…. What is the issue?
Thank you very much,
Kathryn
On 1/11/13 6:55 AM, Sun, Wenping [USA] wrote:
Hi Jennifer,
Thanks for the information on MACS tools.
Yes, I forgot to mention that I used bowtie mapped files as the input.
Thank you very much,
Kathryn
From: Jennifer Jackson [mailto:jen@bx.psu.edu] Sent: Friday, January 11, 2013 3:48 AM To: Sun, Wenping [USA] Cc: galaxy-user@bx.psu.edu Subject: [External] Re: [galaxy-user] macs error for chipseq data
Hello Kathryn,
This is occurring on your local Galaxy install? Have you installed the actual MACS tool and set up the proper configuration paths? Details for how to do this are in these wikis: http://wiki.galaxyproject.org/Admin/Config/Tool%20Dependencies http://wiki.galaxyproject.org/Admin/Tools/Tool%20Dependencies
Apart from that, I should let you know that prior to running MACS, groomed fastq datasets first need to be mapped. An example can be found in our Using Galaxy paper, protocol #3. Links to the paper and supplemental materials (including a screencast walk-through) are available here: https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012
If you need more help with your local install, directing questions to the galaxy-dev@bx.psu.edu mailing list would be best,
Thanks!
Jen Galaxy team
On 1/10/13 1:14 PM, Sun, Wenping [USA] wrote:
Dear galaxy users,
I’ve encountered the error while running macs on galaxy for chipseq data. I used fastq groomed files as input and had the following error
An error occurred running this job: /bin/sh: macs: not found
Anybody can kindly provide some hints?
Thanks,
Kathryn
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
--
Jennifer Hillman-Jackson
Galaxy Support and Training
-- Jennifer Hillman-Jackson Galaxy Support and Training http://galaxyproject.org
___________________________________________________________ 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:
___________________________________________________________ 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:
participants (6)
-
Dannon Baker -
Dannon Baker -
James Taylor -
Jennifer Jackson -
Quang Trinh -
Sun, Wenping [USA]