Re: [galaxy-dev] Hey, I got some problem using galaxy, If you have a time, I hope your help..!!

2015-10-28 Thread Gildas Le Corguillé 

Hello Yoong,

I quickly see 3 mistakes :
 - you use interpreter="python" but if so, you need to put your scripts 
in the same directory of your .xml. If you really want to use the full 
absolute path, delete the interpreter argument.
 - you don't need $alignments.files_path in your command. $alignments 
seems enough.
 - you describe many outputs although you just use one of them 
($alignments). So, try to comment the others.


Some clues for you :)

Gildas


Le 28/10/2015 12:27, Greg Von Kuster a écrit :

Hello Yoong,

The best place to ask questions like this is the Galaxy Dev mailing 
list (galaxy-dev@lists.galaxyproject.org 
).  There are many 
developers that support this mailing list, so you  will undoutedly 
receive optimal answers to any of your questions.  I’ve forwarded your 
current questions to the mailing list.


Regards,

Greg Von Kuster

On Oct 28, 2015, at 12:56 AM, 홍윤지 > wrote:


hey, my name is yoong in korean student .
i'd like to run the program name Mapsplice2, so i made a xml file, 
and submit that


this is my xml file..




MapSplice2 Description


/home/yoong/galaxy/tools/MapSplice-v2.1.9/mapsplice.py -o 
$alignments.files_path -p 20 --qual-scale phred33 --bam --fusion -c 
/home/yoong/1_reference/hg19 -x /home/yoong/1_reference/BowtieIndex 
-1 $input_reads_1 -2 $input_reads_2











label="fusions_candidates.txt"/>







Help



and, look at the report error, there is no special error... what's 
was the problom..? Do I something wrong ?...

plz help me...!! Thank you ...




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Re: [galaxy-dev] Hey, I got some problem using galaxy, If you have a time, I hope your help..!!

2015-10-28 Thread Greg Von Kuster 
Hello Yoong,

The best place to ask questions like this is the Galaxy Dev mailing list 
(galaxy-dev@lists.galaxyproject.org).  There are many developers that support 
this mailing list, so you  will undoutedly receive optimal answers to any of 
your questions.  I’ve forwarded your current questions to the mailing list.

Regards,

Greg Von Kuster

> On Oct 28, 2015, at 12:56 AM, 홍윤지  wrote:
> 
> hey, my name is yoong in korean student .
> i'd like to run the program name Mapsplice2, so i made a xml file, and submit 
> that
> 
> this is my xml file..
> 
> 
> 
> 
> MapSplice2 Description
> 
> 
> /home/yoong/galaxy/tools/MapSplice-v2.1.9/mapsplice.py -o 
> $alignments.files_path -p 20 --qual-scale phred33 --bam --fusion -c 
> /home/yoong/1_reference/hg19 -x /home/yoong/1_reference/BowtieIndex -1 
> $input_reads_1 -2 $input_reads_2
> 
> 
> 
> 
> 
> 
> 
> 
> 
>  label="fusions_candidates.txt"/>
> 
> 
> 
> 
> 
> 
> Help
> 
> 
> 
> and, look at the report error, there is no special error... what's was the 
> problom..? Do I something wrong ?... 
> plz help me...!! Thank you ...

___
Please keep all replies on the list by using "reply all"
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  http://galaxyproject.org/search/mailinglists/