Re: [galaxy-dev] building indexes

2016-10-03 Thread Devon Ryan 

Have you tried the bwtsw method in the bwa mem data manager?

Regarding the 2bit file, even if you make it, are you sure the 
downstream tool(s) will handle the missing chromosomes/contigs?


Maybe you should use the primary assembly instead (at least for the 2bit 
file).


Devon

On 10/03/2016 03:50 PM, Nikolaos Tur wrote:

Hi,

I try to build indexes for ch38 (GRCh38.84 Toplevel) using data 
managers for BWA-MEM and TwoBit.

Both failed.

Error building index:
Error in faToTwoBit, index overflow at CHR_HSCHR4_5_CTG12. The 2bit 
format does not support indexes larger than 4Gb,

please split up into smaller files.

[bwa_index] Update BWT... [bwt_bwtupdate_core] Failed to allocate 
46629609168 bytes at bwtindex.c line 135: Cannot allocate memory

Error building index.

So, how to split genome for TwoBit and how much RAM is needed for BWA 
indexes? These errors are from runs on machine with 45GB RAM.


Thanx,
Nikolaos


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--
Devon Ryan, PhD
Bioinformatician / Data manager
Bioinformatics Core Facility
Max Planck Institute for Immunobiology and Epigenetics
Email: dprya...@gmail.com

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Re: [galaxy-dev] R dependency problems with readline libraries

2016-10-03 Thread Tiago Antao 
Is there any part of conda here? This reminds me of the exact same 
problems that I had with a few libs (readline for example) and conda 
linkage.


On 2016-10-03 13:37, Nicola Soranzo wrote:

I suppose this is the same as
https://github.com/galaxyproject/tools-devteam/issues/100 , just for a
different R version.

Cheers,
Nicola

On 03/10/16 20:10, Nikolaos Tur wrote:


Hi,

installation of deseq2 1.10.0 causes next problem:



/home/galaxy/galaxy/tools/dependencies/R/3.2.1/iuc/package_r_3_2_1/d9f7d84125b7/lib/R/bin/exec/R:

error while loading shared libraries: libreadline.so.6: cannot open
shared object file: No such file or directory Installed tool
dependencies: deseq2

R 3.2.1 installed without problems
readline 6.3 installed too

why does it happen? Is something missing?

The same readline dependency problem from R happen also during
installation of packages bioconductor_limma & bioconductor_edger

Meanwhile dseq2 1.2.10 depended on R 3.0.3 has installed but shown
warnings and also related to R:



/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld:

warning: libgfortran.so.1, needed by


/home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so,

not found (try using -rpath or -rpath-link)


/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld:

warning: libreadline.so.6, needed by


/home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so,

not found (try using -rpath or -rpath-link)

Thanx,
Nikolaos

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Re: [galaxy-dev] R dependency problems with readline libraries

2016-10-03 Thread Nicola Soranzo 
I suppose this is the same as 
https://github.com/galaxyproject/tools-devteam/issues/100 , just for a 
different R version.


Cheers,
Nicola


On 03/10/16 20:10, Nikolaos Tur wrote:

Hi,

installation of deseq2 1.10.0 causes next problem:

/home/galaxy/galaxy/tools/dependencies/R/3.2.1/iuc/package_r_3_2_1/d9f7d84125b7/lib/R/bin/exec/R: 
error while loading shared libraries: libreadline.so.6: cannot open 
shared object file: No such file or directory Installed tool 
dependencies: deseq2


R 3.2.1 installed without problems
readline 6.3 installed too

why does it happen? Is something missing?

The same readline dependency problem from R happen also during 
installation of packages bioconductor_limma & bioconductor_edger


Meanwhile dseq2 1.2.10 depended on R 3.0.3 has installed but shown 
warnings and also related to R:


/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: 
warning: libgfortran.so.1, needed by 
/home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so, 
not found (try using -rpath or -rpath-link)
/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: 
warning: libreadline.so.6, needed by 
/home/galaxy/galaxy/tools/dependencies/R/3.0.3/iuc/package_r_3_0_3/afc48696ee5c/lib/R/lib/libR.so, 
not found (try using -rpath or -rpath-link)


Thanx,
Nikolaos


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Re: [galaxy-dev] Install error of package_bioconductor_limma_3_28_10

2016-10-03 Thread Alexandre Defelicibus 
Hi Nicola,

I've created the issue!
https://github.com/galaxyproject/tools-iuc/issues/979

Cheers,
Alexandre

2016-10-03 12:23 GMT-03:00 Nicola Soranzo :

> Hi Alexandre,
> thanks for your email! Can you please open an issue for this at
> https://github.com/galaxyproject/tools-iuc/issues/new ?
>
> Cheers,
> Nicola
>
>
> On 03/10/16 15:37, Alexandre Defelicibus wrote:
>
> Hi all,
>
> I got this error when I tried to install the package package_bioconductor_
> limma_3_28_10
> 
> :
> Error downloading from URL
> https://depot.galaxyproject.org/software/limma/limma_3.28.
> 10_src_all.tar.gz:
> HTTP Error 404: Not Found
>
> Could someone help me?
>
> Best regards,
>
> Alexandre
>
>
>
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-- 
Alexandre Defelicibus, Me.
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Re: [galaxy-dev] Install error of package_bioconductor_limma_3_28_10

2016-10-03 Thread Nicola Soranzo 

Hi Alexandre,
thanks for your email! Can you please open an issue for this at 
https://github.com/galaxyproject/tools-iuc/issues/new ?


Cheers,
Nicola

On 03/10/16 15:37, Alexandre Defelicibus wrote:

Hi all,

I got this error when I tried to install the package 
package_bioconductor_limma_3_28_10 
:

Error downloading from URL
https://depot.galaxyproject.org/software/limma/limma_3.28.10_src_all.tar.gz:
HTTP Error 404: Not Found

Could someone help me?

Best regards,

Alexandre



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[galaxy-dev] News of the Galaxy: October 2016

2016-10-03 Thread Dave Clements 
Hello all,

The *October Galaxy News
* is hot off the
presses and *upcoming events
* are
prominent:

   -

   *Galaxy training contribution fest
   
*:
   October 6-7, Online
   -

   *Swiss-German Galaxy Days
   
*:
   October 20-21, Freiburg, Germany
   -

   *Galaxy & Hacktoberfest
   
*:
   Month of October, online
   -

   *Bioconda Contribution Fest
   
*:
   November 2-3, Online
   
   -

   *Galaxy Admin Training
   
*:
   November 7-11, Salt Lake City, Utah.
   -

  *On time registration ends October 16*
  -

   *Galaxy Australasia Meeting (GAMe 2017)
   
*:
   February 3-9, Melbourne, Victoria, Australia.
   -

  *Registration and abstract submission are now open.*
  -

   And of course, other upcoming events
   
too

There are also 117 new publications

(including
six featured pubs), four open positions
, two
new public Galaxy servers and one new semi-public Galaxy service

, new releases of galaxy-lib & Planemo
, new
TooShed contributions
,
and other news
 too.

We hope to see you in Freiburg, Salt Lake, Melbourne, online, and around
the world,

Dave Clements and the Galaxy Team


-- 
http://galaxyproject.org/
http://getgalaxy.org/
http://usegalaxy.org/
https://wiki.galaxyproject.org/
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[galaxy-dev] Install error of package_bioconductor_limma_3_28_10

2016-10-03 Thread Alexandre Defelicibus 
Hi all,

I got this error when I tried to install the package
package_bioconductor_limma_3_28_10

:
Error downloading from URL
https://depot.galaxyproject.org/software/limma/limma_3.28.10_src_all.tar.gz:
HTTP Error 404: Not Found

Could someone help me?

Best regards,

Alexandre
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[galaxy-dev] building indexes

2016-10-03 Thread Nikolaos Tur 
Hi,

I try to build indexes for ch38 (GRCh38.84 Toplevel) using data managers
for BWA-MEM and TwoBit.
Both failed.

Error building index:
Error in faToTwoBit, index overflow at CHR_HSCHR4_5_CTG12. The 2bit format
does not support indexes larger than 4Gb,
please split up into smaller files.

[bwa_index] Update BWT... [bwt_bwtupdate_core] Failed to allocate
46629609168 bytes at bwtindex.c line 135: Cannot allocate memory
Error building index.

So, how to split genome for TwoBit and how much RAM is needed for BWA
indexes? These errors are from runs on machine with 45GB RAM.

Thanx,
Nikolaos
___
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