[galaxy-dev] htseq_count version 0.6.1p1 dated (2016-09-21) and (2015-07-28)

2016-12-01 Thread Raphenya, Amogelang 



Hi,


Both versions are not working. I’m getting the following error;



[bam_header_read] EOF marker is absent. The input is probably truncated.
[sam_header_read2] 194 sequences loaded.
[sam_read1] reference '' is recognized as '*'.
Parse error at line 1: invalid CIGAR character

Any ideas?


Cheers.




Amos Raphenya, B.Eng 

Bioinformatics Software Developer

Department of Biochemistry & Biomedical Sciences

McMaster University, MDCL 2317

p: (905) 525-9140

a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1

e:  raphe...@mcmaster.ca

skype: amos_raphenya



















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[galaxy-dev] Error for Picard CollectInsertSizeMetrics

2016-10-31 Thread Raphenya, Amogelang 



Hi,


Any ideas how to solve this error for CollectInsertSizeMetrics:



Fatal error: Exit code 1 ()
Picked up _JAVA_OPTIONS: -Xmx2048m -Xms256m
Exception in thread "main" htsjdk.samtools.SAMException: Reference sequence (424) not found in ../../galaxy/tool-data/grch38/seq/grch38.fa


	at htsjdk.samtools.reference.ReferenceSequenceFileWalker.get(ReferenceSequenceFileWalker.java:98)
	at picard.analysis.SinglePassSamProgram.makeItSo(SinglePassSamProgram.java:110)
	at picard.analysis.SinglePassSamProgram.doWork(SinglePassSamProgram.java:53)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)



Cheers.




Amos Raphenya, B.Eng 

Bioinformatics Software Developer

Department of Biochemistry & Biomedical Sciences

McMaster University, MDCL 2317

p: (905) 525-9140

a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1

e:  raphe...@mcmaster.ca

skype: amos_raphenya


















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[galaxy-dev] STACKS error

2016-05-20 Thread Raphenya, Amogelang 



Anyone encountered this error?



Fatal error: Exit code 1 (Error in Stacks Process radtag execution)
Traceback (most recent call last):
  File "/galaxylab/production/new/shed_tools/toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/STACKS_procrad.py", line 16, in 
from stacks import *
  File "/galaxylab/production/new/shed_tools/toolshed.g2.bx.psu.edu/repos/cmonjeau/stacks/0e0ff9e9c761/stacks/stacks.py", line 19, in 
from galaxy.datatypes.checkers import *
ImportError: No module named checkers


Cheers.






Amos Raphenya, B.Eng 

Bioinformatics Software Developer

Department of Biochemistry & Biomedical Sciences

McMaster University, MDCL 2317

p: (905) 525-9140

a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1

e:  raphe...@mcmaster.ca

skype: amos_raphenya



















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Re: [galaxy-dev] tmp directory

2016-03-01 Thread Raphenya, Amogelang 



Is there a script that is used to clean up database/tmp














Amos Raphenya 
Bioinformatics Software Developer
Department of Biochemistry & Biomedical Sciences
McMaster University, MDCL 2317
p: (905) 525-9140 ext: 22787
a: 1280 Main St W.,Hamilton,
 Ontario, Canada L8S 4K1
e:  raphe...@mcmaster.ca 
skype: amos_raphenya













On Feb 29, 2016, at 10:21 AM, Björn Grüning <bjoern.gruen...@gmail.com> wrote:

Hi,

if you are not overwriting this value with a object_store setting, it
defaults to 'database/tmp' as written in galaxy.ini. The values are the
default values which you see.

Ciao,
Bjoern

Am 29.02.2016 um 16:19 schrieb Raphenya, Amogelang:
Hi All,

Where are the temporary files stored if the line below is commented out?

|# Temporary files are stored in this directory. new_file_path =
database/tmp|


Thank you.

/
/ 
/*Amos Raphenya* /
/Bioinformatics Software Developer/
/Department of Biochemistry & Biomedical Sciences/
/McMaster University, MDCL //2317/
/p: (905) 525-9140 //ext: //22787/
/a: 1280 Main St W.,Hamilton, Ontario, Canada L8S 4K1/
/e:  raphe...@mcmaster.ca <mailto:raphe...@mcmaster.ca> /
/skype: amos_raphenya/




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[galaxy-dev] tmp directory

2016-02-29 Thread Raphenya, Amogelang 



Hi All,


Where are the temporary files stored if the line below is commented out?



# Temporary files are stored in this directory.
new_file_path = database/tmp



Thank you.













Amos Raphenya 
Bioinformatics Software Developer
Department of Biochemistry & Biomedical Sciences
McMaster University, MDCL 2317
p: (905) 525-9140 ext: 22787
a: 1280 Main St W.,Hamilton,
 Ontario, Canada L8S 4K1
e:  raphe...@mcmaster.ca 
skype: amos_raphenya















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[galaxy-dev] Lost prostgresql database

2016-02-25 Thread Raphenya, Amogelang 



Hi All,


Our server hard drive failed and we lost the database which was running galaxy instance.


But we did NOT loose all the data i.e all the files are there under the /galaxy-dist
directory.


Is there a way to reconstruct the database using the data itself.


Please help.













Amos Raphenya 
Bioinformatics Software Developer
Department of Biochemistry & Biomedical Sciences
McMaster University, MDCL 2317
p: (905) 525-9140 ext: 22787
a: 1280 Main St W.,Hamilton,
 Ontario, Canada L8S 4K1
e:  raphe...@mcmaster.ca 
skype: amos_raphenya














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[galaxy-dev] Error sorting tophat accepted hits BAM file by name

2016-02-17 Thread Raphenya, Amogelang 



Hi Guys,


I’m getting error shown below, when sorting tophat accepted hits BAM file by name using
samtools_sort version 1.0.2  (by iuc)



Program: samtools (Tools for alignments in the SAM format)
Version: 0.1.19-44428cd



Command:


samtools sort -n "../../database/files/036/dataset_36372.dat" foo 2>&1 || echo "Error running samtools sort." >&2 ; mv foo.bam "../../database/files/036/dataset_36665.dat"


stdout:

[bam_sort_core] merging from 33 files...
[bam_index_core] the alignment is not sorted (HWI-D00351:251:C80TWANXX:1:1101:1081:98020): 15-th chr > 5-th chr
[bam_index_build2] fail to index the BAM file.
stderr:
Aborted (core dumped)Any ideas?














Amos Raphenya 
Bioinformatics Software Developer
Department of Biochemistry & Biomedical Sciences
McMaster University, MDCL 2317
p: (905) 525-9140 ext: 22787
a: 1280 Main St W.,Hamilton,
 Ontario, Canada L8S 4K1
e:  raphe...@mcmaster.ca 
skype: amos_raphenya















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[galaxy-dev] Loading or Upload Large datasets into Galaxy History

2016-01-28 Thread Raphenya, Amogelang 



Hi All,


Is there a faster way to upload or load large datasets into galaxy history without using FTP?


I tried Upload_local_file (to current history) and it doesn’t upload
.gz files correctly as compared to when using Upload_file
(from your computer).


Cheers.













Amos Raphenya 
Bioinformatics Software Developer
Department of Biochemistry & Biomedical Sciences
McMaster University, MDCL 2317
p: (905) 525-9140 ext: 22787
a: 1280 Main St W.,Hamilton,
 Ontario, Canada L8S 4K1
e:  raphe...@mcmaster.ca 
skype: amos_raphenya














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Re: [galaxy-dev] Adding a5_pipeline.pl to galaxy

2016-01-22 Thread Raphenya, Amogelang 



It works! Thank you Gildas!













Amos Raphenya 
Bioinformatics Software Developer
Department of Biochemistry & Biomedical Sciences
McMaster University, MDCL 2317
p: (905) 525-9140 ext: 22787
a: 1280 Main St W.,Hamilton,
 Ontario, Canada L8S 4K1
e:  raphe...@mcmaster.ca 
skype: amos_raphenya













On Jan 22, 2016, at 9:25 AM, Gildas Le Corguillé  wrote:






A5 output fastQ










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[galaxy-dev] Adding a5_pipeline.pl to galaxy

2016-01-22 Thread Raphenya, Amogelang 



Hi All,


I have a problem getting all the outputs in galaxy.


My xml config file looks like this:




 id="a5_miseq" name="A5 MiSeq" version="0.1.0">



  
assemble microbial fastQ to fatsA



  
 interpreter="perl">a5_pipeline.pl ${file1} ${file2} ${output}






 


   
 format="fastq" name="file1" type="data" label="Fastq Sequence files"/>

   
 format="fastq" name="file2" type="data" label="Fastq Sequence files"/>

 











output.contigs.fasta  



output.contigs.qvl  



output.raw1.pe.sort.bam  



output.tmplibs 



output.assembly_stats.csv  



output.contigs.fastq  



output.ec.fastq.gz   



output.raw1.pe.sort.bam.bai  



output.s1  



output.s2   




-->



 



     format="fasta" name="output" label=“A5 output fastA"/>

   
 format="fastq" name="output" label=“A5 output fastQ”/>













I get the following error when running the tool:



../database/files/000/dataset_733.dat already exists and is not a directory.
Please specify a new file path for a base name after the library file or FastQ files.



Any ideas on how to get all the output or some output?



Cheers.















Amos Raphenya 
Bioinformatics Software Developer
Department of Biochemistry & Biomedical Sciences
McMaster University, MDCL 2317
p: (905) 525-9140 ext: 22787
a: 1280 Main St W.,Hamilton,
 Ontario, Canada L8S 4K1
e:  raphe...@mcmaster.ca 
skype: amos_raphenya














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[galaxy-dev] security: brute force login

2016-01-04 Thread Raphenya, Amogelang 



Hi All,


How can I prevent brute force login attack on the login page?
















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