Recompile transabyss question
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Brian Novogradac
Jun 7, 2016, 10:00:34 AM6/7/16
to Trans-ABySS
I need to recompile to increase default kmer size. Do i need to do a complete uninstall or can i just recompile and it will overwrite the existing transabyss
Ka Ming Nip
Jun 7, 2016, 11:59:10 AM6/7/16
to trans...@googlegroups.com
You just need to reconfigure and recompile ABySS. Your Trans-ABySS installation should be fine.
--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Brian Novogradac [brian.no...@gmail.com]
Sent: June 7, 2016 7:00 AM
To: Trans-ABySS
Subject: Recompile transabyss question
I need to recompile to increase default kmer size. Do i need to do a complete uninstall or can i just recompile and it will overwrite the existing transabyss
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--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Brian Novogradac [brian.no...@gmail.com]
Sent: June 7, 2016 7:00 AM
To: Trans-ABySS
Subject: Recompile transabyss question
I need to recompile to increase default kmer size. Do i need to do a complete uninstall or can i just recompile and it will overwrite the existing transabyss
You received this message because you are subscribed to the Google Groups "Trans-ABySS" group.
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Brian Novogradac
Jun 7, 2016, 3:17:27 PM6/7/16
to Trans-ABySS
ok, thanks would it still be recommended to uninstall the existing version or can i recompile abyss on top of current installation? Also is it possible to have two different compiled installs of abyss?
Sorry for a ll the questions im learning all this from scratch and starting new.
Brian
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Ka Ming Nip
Jun 7, 2016, 4:23:49 PM6/7/16
to trans...@googlegroups.com
No problem! There is no need to uninstall.
Reconfigure with a large maxk, eg.
./configure --enable-maxk=96
Then, compiling would overwrite the old binaries. However, more memory is allocated per kmer than previously when maxk was 64. An assembly at k32 would now be using more memory than before.
In this case, you could install ABySS with different maxk into different directories, eg.
/home/kmnip/bin/abyss/k32
/home/kmnip/bin/abyss/k64
/home/kmnip/bin/abyss/k96
Just make sure you add the appropriate path to your environment each time, ie. with the `export` command:
for k33 to 64:
export PATH=/home/kmnip/bin/abyss/k64:$PATH
for k65 to 96:
export PATH=/home/kmnip/bin/abyss/k96:$PATH
Ka Ming
--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Brian Novogradac [brian.no...@gmail.com]
Sent: June 7, 2016 12:17 PM
To: Trans-ABySS
Subject: Re: Recompile transabyss question
ok, thanks would it still be recommended to uninstall the existing version or can i recompile abyss on top of current installation? Also is it possible to have two different compiled installs of abyss?
Sorry for a ll the questions im learning all this from scratch and starting new.
Brian
On Tuesday, June 7, 2016 at 11:59:10 AM UTC-4, Ka Ming Nip wrote:
You just need to reconfigure and recompile ABySS. Your Trans-ABySS installation should be fine.
--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com<javascript:> [trans...@googlegroups.com<javascript:>] On Behalf Of Brian Novogradac [brian.no...@gmail.com<javascript:>]
Reconfigure with a large maxk, eg.
./configure --enable-maxk=96
Then, compiling would overwrite the old binaries. However, more memory is allocated per kmer than previously when maxk was 64. An assembly at k32 would now be using more memory than before.
In this case, you could install ABySS with different maxk into different directories, eg.
/home/kmnip/bin/abyss/k32
/home/kmnip/bin/abyss/k64
/home/kmnip/bin/abyss/k96
Just make sure you add the appropriate path to your environment each time, ie. with the `export` command:
for k33 to 64:
export PATH=/home/kmnip/bin/abyss/k64:$PATH
for k65 to 96:
export PATH=/home/kmnip/bin/abyss/k96:$PATH
Ka Ming
--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
From: trans...@googlegroups.com [trans...@googlegroups.com] On Behalf Of Brian Novogradac [brian.no...@gmail.com]
To: Trans-ABySS
Subject: Re: Recompile transabyss question
ok, thanks would it still be recommended to uninstall the existing version or can i recompile abyss on top of current installation? Also is it possible to have two different compiled installs of abyss?
Sorry for a ll the questions im learning all this from scratch and starting new.
Brian
On Tuesday, June 7, 2016 at 11:59:10 AM UTC-4, Ka Ming Nip wrote:
You just need to reconfigure and recompile ABySS. Your Trans-ABySS installation should be fine.
--
Ka Ming Nip
GrasPods Wellness Coordinator
Graduate Student | Dr. Inanc Birol Lab (BTL)
Canada's Michael Smith Genome Sciences Centre
________________________________________
Sent: June 7, 2016 7:00 AM
To: Trans-ABySS
Subject: Recompile transabyss question
I need to recompile to increase default kmer size. Do i need to do a complete uninstall or can i just recompile and it will overwrite the existing transabyss
--
You received this message because you are subscribed to the Google Groups "Trans-ABySS" group.
To unsubscribe from this group and stop receiving emails from it, send an email to trans-abyss...@googlegroups.com<javascript:><mailto:trans-abyss...@googlegroups.com<javascript:>>.
To: Trans-ABySS
Subject: Recompile transabyss question
I need to recompile to increase default kmer size. Do i need to do a complete uninstall or can i just recompile and it will overwrite the existing transabyss
--
You received this message because you are subscribed to the Google Groups "Trans-ABySS" group.
--
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Brian Novogradac
Jun 9, 2016, 10:40:52 AM6/9/16
to Trans-ABySS
Thanks!!!
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