date:20170811

Re: [galaxy-dev] Bowtie2 index building

2017-08-11 Thread Deepak Tanwar

Hi Björn,

That’s right! It was quiet strange. I need to extend the memory and cores usage 
via command line.

Thank you so much!

Deepak


> On Aug 11, 2017, at 10:00, Björn Grüning  wrote:
> 
> Hi,
> 
> it seems that your Docker Box only gets 1GB :(
> 
> please re-check the configs.
> Sorry to be not more helpful!
> Bjoern
> 
> On 11.08.2017 15:55, Deepak Tanwar wrote:
>> Also, I am running this container on a Mac Pro using Kitematic and I
>> have docker preference set to use 12 cores and 64 GB RAM.
>> 
>> Thanks,
>> Deepak
>> 
>> 
>>> On Aug 11, 2017, at 9:54 AM, Deepak Tanwar >> > wrote:
>>> 
>>> Hi Björn,
>>> 
>>> If I do docker stats:
>>> CONTAINER   CPU %   MEM USAGE / LIMIT MEM %  
>>>NET I/O BLOCK I/O   PIDS
>>> dd4da10c0a546.16%   690.9MiB / 995.8MiB   69.38%  
>>>   158kB / 785kB   11.4GB / 81MB   106
>>> 
>>> And, after ssh into docker machine:
>>> 
>>> FilesystemSize  Used Available Use% Mounted on
>>> tmpfs   896.2M186.6M709.6M  21% /
>>> tmpfs   497.9M476.0K497.4M   0% /dev/shm
>>> /dev/sda1   282.7G 14.9G253.2G   6% /mnt/sda1
>>> cgroup  497.9M 0497.9M   0% /sys/fs/cgroup
>>> Users   931.0G683.8G247.2G  73% /Users
>>> /dev/sda1   282.7G 14.9G253.2G   6%
>>> /mnt/sda1/var/lib/docker/aufs
>>> 
>>> Best regards,
>>> Deepak
>>> 
>>> 
 On Aug 11, 2017, at 9:39 AM, Björn Grüning > wrote:
 
 Hi Deepak,
 
 how are you running this Container?
 Can you check how many memory you have inside the container?
 
 Cheers,
 Bjoern
 
 On 11.08.2017 15:35, Deepak Tanwar wrote:
> Hello,
> 
> I am trying to build Bowtie2 index for hg19.
> I a using Docker image of Galaxy.
> 
> Computer I am using have 12 cores and 64 GB of RAM.
> 
> Error I am getting is:
> 
> Fatal error: Exit code 1 ()
> Building a SMALL index
> Could not allocate space for a joined string of 2897310462 elements.
> Switching to a packed string representation.
> Building a SMALL index
> Could not find approrpiate bmax/dcv settings for building this index.
> Already tried a packed string representation.
> Please try indexing this reference on a computer with more memory.
> Error: Encountered internal Bowtie 2 exception (#1)
> Command: bowtie2-build --wrapper basic-0
> /export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
> fa.fa hg19 fa
> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
> Error building index.
> 
> Please help!
> 
> Thank you,
> Deepak
> 
> 
> 
> ___
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>>> 
>>> ___
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>> 

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Re: [galaxy-dev] Bowtie2 index building

2017-08-11 Thread Björn Grüning

Hi,

it seems that your Docker Box only gets 1GB :(

please re-check the configs.
Sorry to be not more helpful!
Bjoern

On 11.08.2017 15:55, Deepak Tanwar wrote:
> Also, I am running this container on a Mac Pro using Kitematic and I
> have docker preference set to use 12 cores and 64 GB RAM.
> 
> Thanks,
> Deepak
> 
> 
>> On Aug 11, 2017, at 9:54 AM, Deepak Tanwar > > wrote:
>>
>> Hi Björn,
>>
>> If I do docker stats:
>> CONTAINER   CPU %   MEM USAGE / LIMIT MEM %  
>> NET I/O BLOCK I/O   PIDS
>> dd4da10c0a546.16%   690.9MiB / 995.8MiB   69.38%  
>>158kB / 785kB   11.4GB / 81MB   106
>>
>> And, after ssh into docker machine:
>>
>> FilesystemSize  Used Available Use% Mounted on
>> tmpfs   896.2M186.6M709.6M  21% /
>> tmpfs   497.9M476.0K497.4M   0% /dev/shm
>> /dev/sda1   282.7G 14.9G253.2G   6% /mnt/sda1
>> cgroup  497.9M 0497.9M   0% /sys/fs/cgroup
>> Users   931.0G683.8G247.2G  73% /Users
>> /dev/sda1   282.7G 14.9G253.2G   6%
>> /mnt/sda1/var/lib/docker/aufs
>>
>> Best regards,
>> Deepak
>>
>>
>>> On Aug 11, 2017, at 9:39 AM, Björn Grüning >> > wrote:
>>>
>>> Hi Deepak,
>>>
>>> how are you running this Container?
>>> Can you check how many memory you have inside the container?
>>>
>>> Cheers,
>>> Bjoern
>>>
>>> On 11.08.2017 15:35, Deepak Tanwar wrote:
 Hello,

 I am trying to build Bowtie2 index for hg19.
 I a using Docker image of Galaxy.

 Computer I am using have 12 cores and 64 GB of RAM.

 Error I am getting is:

 Fatal error: Exit code 1 ()
 Building a SMALL index
 Could not allocate space for a joined string of 2897310462 elements.
 Switching to a packed string representation.
 Building a SMALL index
 Could not find approrpiate bmax/dcv settings for building this index.
 Already tried a packed string representation.
 Please try indexing this reference on a computer with more memory.
 Error: Encountered internal Bowtie 2 exception (#1)
 Command: bowtie2-build --wrapper basic-0
 /export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
 fa.fa hg19 fa
 Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
 Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
 Error building index.

 Please help!

 Thank you,
 Deepak

 ___
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>>
>> ___
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>>
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> 
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Re: [galaxy-dev] Bowtie2 index building

2017-08-11 Thread Deepak Tanwar

Hi Björn,

If I do docker stats:
CONTAINER   CPU %   MEM USAGE / LIMIT MEM % 
  NET I/O BLOCK I/O   PIDS
dd4da10c0a546.16%   690.9MiB / 995.8MiB   69.38%
  158kB / 785kB   11.4GB / 81MB   106

And, after ssh into docker machine:

FilesystemSize  Used Available Use% Mounted on
tmpfs   896.2M186.6M709.6M  21% /
tmpfs   497.9M476.0K497.4M   0% /dev/shm
/dev/sda1   282.7G 14.9G253.2G   6% /mnt/sda1
cgroup  497.9M 0497.9M   0% /sys/fs/cgroup
Users   931.0G683.8G247.2G  73% /Users
/dev/sda1   282.7G 14.9G253.2G   6% 
/mnt/sda1/var/lib/docker/aufs

Best regards,
Deepak


On Aug 11, 2017, at 9:39 AM, Björn Grüning 
> wrote:

Hi Deepak,

how are you running this Container?
Can you check how many memory you have inside the container?

Cheers,
Bjoern

On 11.08.2017 15:35, Deepak Tanwar wrote:
Hello,

I am trying to build Bowtie2 index for hg19.
I a using Docker image of Galaxy.

Computer I am using have 12 cores and 64 GB of RAM.

Error I am getting is:

Fatal error: Exit code 1 ()
Building a SMALL index
Could not allocate space for a joined string of 2897310462 elements.
Switching to a packed string representation.
Building a SMALL index
Could not find approrpiate bmax/dcv settings for building this index.
Already tried a packed string representation.
Please try indexing this reference on a computer with more memory.
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0
/export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
fa.fa hg19 fa
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Error building index.

Please help!

Thank you,
Deepak



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Re: [galaxy-dev] Bowtie2 index building

2017-08-11 Thread Björn Grüning

Hi Deepak,

how are you running this Container?
Can you check how many memory you have inside the container?

Cheers,
Bjoern

On 11.08.2017 15:35, Deepak Tanwar wrote:
> Hello,
> 
> I am trying to build Bowtie2 index for hg19.
> I a using Docker image of Galaxy.
> 
> Computer I am using have 12 cores and 64 GB of RAM.
> 
> Error I am getting is:
> 
> Fatal error: Exit code 1 ()
> Building a SMALL index
> Could not allocate space for a joined string of 2897310462 elements.
> Switching to a packed string representation.
> Building a SMALL index
> Could not find approrpiate bmax/dcv settings for building this index.
> Already tried a packed string representation.
> Please try indexing this reference on a computer with more memory.
> Error: Encountered internal Bowtie 2 exception (#1)
> Command: bowtie2-build --wrapper basic-0
> /export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
> fa.fa hg19 fa 
> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
> Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
> Error building index. 
> 
> Please help!
> 
> Thank you,
> Deepak
> 
> 
> 
> ___
> 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:
>   https://lists.galaxyproject.org/
> 
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/
> 
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[galaxy-dev] Bowtie2 index building

2017-08-11 Thread Deepak Tanwar

Hello,

I am trying to build Bowtie2 index for hg19.
I a using Docker image of Galaxy.

Computer I am using have 12 cores and 64 GB of RAM.

Error I am getting is:

Fatal error: Exit code 1 ()
Building a SMALL index
Could not allocate space for a joined string of 2897310462 elements.
Switching to a packed string representation.
Building a SMALL index
Could not find approrpiate bmax/dcv settings for building this index.
Already tried a packed string representation.
Please try indexing this reference on a computer with more memory.
Error: Encountered internal Bowtie 2 exception (#1)
Command: bowtie2-build --wrapper basic-0 
/export/galaxy-central/database/job_working_directory/000/113/dataset_80_files/hg19
 fa.fa hg19 fa
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.3.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.4.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.1.bt2" file written during aborted indexing attempt.
Deleting "hg19 fa.2.bt2" file written during aborted indexing attempt.
Error building index.

Please help!

Thank you,
Deepak

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Re: [galaxy-dev] Data manager for ncbi_blast_plus in the main tool shed?

2017-08-11 Thread Peter Cock

Hi David,

Daniel Blankenberg wrote one (CC'd):

https://github.com/peterjc/galaxy_blast/tree/master/data_managers/ncbi_blastdb

http://testtoolshed.g2.bx.psu.edu/view/blankenberg/data_manager_example_blastdb_ncbi_update_blastdb

I've never used it in production and don't have enough understanding
of it and the Data Manager framework to understand what if anything
needs working on.

Locally we have mirrors of the NCBI blast databases (updated with cron),
local databases for organisms of interest - these are all listed in the
*.loc
files by hand.

Separately, our users can and do make their own databases within
Galaxy using makeblastdb.

Regards,

Peter

On Thu, Aug 10, 2017 at 10:32 PM, David Kovalic  wrote:

> Hi,
>
> Does anyone know if a data manager exists in the tool shed for creating
> and integrating NCBI BLAST+ indices within galaxy?
>
> I can't seem to find it in the tools shed or searching the internet  Surly
> such a tool must exist.
>
> Any info would be greatly appreciated.
>
> Thanks,
>
> David
>
>
>
> David Kovalic Ph.D.   President, Analome
> phone: +314.496.8808
> web: www.analome.com
> email: kova...@analome.com
> 
>
>
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>   http://galaxyproject.org/search/
>
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Re: [galaxy-dev] Installing Galaxy, Conda and Python

2017-08-11 Thread Lachlan Musicman

On 11 August 2017 at 14:33, Lachlan Musicman  wrote:

> Hola,
>
> We are attempting to install Galaxy, from git, version 17.05
>
> We largely have it installed, but seem to be falling over at the
> installation of dependencies.
>
> In particular, conda via Galaxy can't find Gnuplot 4.6, and the conda
> libraries don't show a gnuplot < 5.x
>
> The error:
>


FWIW, we eventually found the problem and solution -
http://dev.list.galaxyproject.org/Problem-with-installing-tools-using-Conda-td4670590.html

It was identical. Looks like there is a rogue supervisord online tutorial
out there that people are want to follow.

cheers
L.


--
"The antidote to apocalypticism is *apocalyptic civics*. Apocalyptic civics
is the insistence that we cannot ignore the truth, nor should we panic
about it. It is a shared consciousness that our institutions have failed
and our ecosystem is collapsing, yet we are still here — and we are
creative agents who can shape our destinies. Apocalyptic civics is the
conviction that the only way out is through, and the only way through is
together. "

*Greg Bloom* @greggish
https://twitter.com/greggish/status/873177525903609857
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Re: [galaxy-dev] Bowtie2 index building

Re: [galaxy-dev] Bowtie2 index building

Re: [galaxy-dev] Bowtie2 index building

Re: [galaxy-dev] Bowtie2 index building

[galaxy-dev] Bowtie2 index building

Re: [galaxy-dev] Data manager for ncbi_blast_plus in the main tool shed?

Re: [galaxy-dev] Installing Galaxy, Conda and Python

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