Re: [galaxy-dev] macs in galaxy
I don't believe so, it looks like they generate a long config script (as you can see in the xml file) and executes that. K On Thu, Sep 8, 2011 at 1:51 PM, Chorny, Ilya wrote: > Is there a python script associated with the macs.xml file? > > ** ** > > *From:* galaxy-dev-boun...@lists.bx.psu.edu [mailto: > galaxy-dev-boun...@lists.bx.psu.edu] *On Behalf Of *Kanwei Li > *Sent:* Wednesday, August 24, 2011 5:41 PM > > *To:* KOH Jia Yu Jayce > *Cc:* galaxy-dev@lists.bx.psu.edu > *Subject:* Re: [galaxy-dev] macs in galaxy > > ** ** > > You can use the MACS wrappers here (for 1.4): > https://bitbucket.org/cistrome/cistrome-harvard/src/779d208c2cbd/tools/peakcalling/ > > > ** ** > > Until we officially add it to our distribution. > > ** ** > > Thanks, > > ** ** > > K > > On Wed, Aug 24, 2011 at 8:32 PM, KOH Jia Yu Jayce > wrote: > > Yes. Thank you for your help J > > > > -Original Message- > *From:* Kanwei Li [mailto:kan...@gmail.com] > *Sent:* Wednesday, August 24, 2011 11:28 PM > *To:* KOH Jia Yu Jayce > *Cc:* galaxy-dev@lists.bx.psu.edu > *Subject:* Re: [galaxy-dev] macs in galaxy > > > > Hi Jayce, > > > > Are you running this on your local instance? It seems you are running MACS > 1.4, which our wrapper does not support yet, but we are planning to add a > wrapper for 1.4 soon. > > > > Thanks, > > > > K > > On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce > wrote: > > In running macs in galaxy, the following error was found > > > > ERROR:root:mfold format error! Your input is '32'. It should be like > '10,30' > > > > A format for mfold like 10,30 is expected… but the default value configured > in xml remains as 32. will there be an updated version of this xml in > future? > > > > Also after altering the default display mfold value to 10,30, type integer > in the param tag for mfold become erroneous. May I ask what is the correct > type for input format 10,30? > > > > Thanks alot > > > > > > > ___ > 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] macs in galaxy
Is there a python script associated with the macs.xml file? From: galaxy-dev-boun...@lists.bx.psu.edu [mailto:galaxy-dev-boun...@lists.bx.psu.edu] On Behalf Of Kanwei Li Sent: Wednesday, August 24, 2011 5:41 PM To: KOH Jia Yu Jayce Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] macs in galaxy You can use the MACS wrappers here (for 1.4): https://bitbucket.org/cistrome/cistrome-harvard/src/779d208c2cbd/tools/peakcalling/ Until we officially add it to our distribution. Thanks, K On Wed, Aug 24, 2011 at 8:32 PM, KOH Jia Yu Jayce mailto:ko...@gis.a-star.edu.sg>> wrote: Yes. Thank you for your help ☺ -Original Message- From: Kanwei Li [mailto:kan...@gmail.com<mailto:kan...@gmail.com>] Sent: Wednesday, August 24, 2011 11:28 PM To: KOH Jia Yu Jayce Cc: galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Subject: Re: [galaxy-dev] macs in galaxy Hi Jayce, Are you running this on your local instance? It seems you are running MACS 1.4, which our wrapper does not support yet, but we are planning to add a wrapper for 1.4 soon. Thanks, K On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce mailto:ko...@gis.a-star.edu.sg>> wrote: In running macs in galaxy, the following error was found ERROR:root:mfold format error! Your input is '32'. It should be like '10,30' A format for mfold like 10,30 is expected… but the default value configured in xml remains as 32. will there be an updated version of this xml in future? Also after altering the default display mfold value to 10,30, type integer in the param tag for mfold become erroneous. May I ask what is the correct type for input format 10,30? Thanks alot ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] macs in galaxy
You can use the MACS wrappers here (for 1.4): https://bitbucket.org/cistrome/cistrome-harvard/src/779d208c2cbd/tools/peakcalling/ Until we officially add it to our distribution. Thanks, K On Wed, Aug 24, 2011 at 8:32 PM, KOH Jia Yu Jayce wrote: > Yes. Thank you for your help J > > > > -Original Message- > *From:* Kanwei Li [mailto:kan...@gmail.com] > *Sent:* Wednesday, August 24, 2011 11:28 PM > *To:* KOH Jia Yu Jayce > *Cc:* galaxy-dev@lists.bx.psu.edu > *Subject:* Re: [galaxy-dev] macs in galaxy > > > > Hi Jayce, > > > > Are you running this on your local instance? It seems you are running MACS > 1.4, which our wrapper does not support yet, but we are planning to add a > wrapper for 1.4 soon. > > > > Thanks, > > > > K > > On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce > wrote: > > In running macs in galaxy, the following error was found > > > > ERROR:root:mfold format error! Your input is '32'. It should be like > '10,30' > > > > A format for mfold like 10,30 is expected… but the default value configured > in xml remains as 32. will there be an updated version of this xml in > future? > > > > Also after altering the default display mfold value to 10,30, type integer > in the param tag for mfold become erroneous. May I ask what is the correct > type for input format 10,30? > > > > Thanks alot > > > > > > > ___ > 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] macs in galaxy
Yes. Thank you for your help :) -Original Message- From: Kanwei Li [mailto:kan...@gmail.com] Sent: Wednesday, August 24, 2011 11:28 PM To: KOH Jia Yu Jayce Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] macs in galaxy Hi Jayce, Are you running this on your local instance? It seems you are running MACS 1.4, which our wrapper does not support yet, but we are planning to add a wrapper for 1.4 soon. Thanks, K On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce mailto:ko...@gis.a-star.edu.sg>> wrote: In running macs in galaxy, the following error was found ERROR:root:mfold format error! Your input is '32'. It should be like '10,30' A format for mfold like 10,30 is expected... but the default value configured in xml remains as 32. will there be an updated version of this xml in future? Also after altering the default display mfold value to 10,30, type integer in the param tag for mfold become erroneous. May I ask what is the correct type for input format 10,30? Thanks alot ___ 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: http://lists.bx.psu.edu/
Re: [galaxy-dev] macs in galaxy
Hi Jayce, Are you running this on your local instance? It seems you are running MACS 1.4, which our wrapper does not support yet, but we are planning to add a wrapper for 1.4 soon. Thanks, K On Wed, Aug 24, 2011 at 4:20 AM, KOH Jia Yu Jayce wrote: > In running macs in galaxy, the following error was found > > > > ERROR:root:mfold format error! Your input is '32'. It should be like > '10,30' > > > > A format for mfold like 10,30 is expected… but the default value configured > in xml remains as 32. will there be an updated version of this xml in > future? > > > > Also after altering the default display mfold value to 10,30, type integer > in the param tag for mfold become erroneous. May I ask what is the correct > type for input format 10,30? > > > > Thanks alot > > > > > > ___ > 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: http://lists.bx.psu.edu/
[galaxy-dev] macs in galaxy
In running macs in galaxy, the following error was found ERROR:root:mfold format error! Your input is '32'. It should be like '10,30' A format for mfold like 10,30 is expected... but the default value configured in xml remains as 32. will there be an updated version of this xml in future? Also after altering the default display mfold value to 10,30, type integer in the param tag for mfold become erroneous. May I ask what is the correct type for input format 10,30? Thanks alot ___ 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/
