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CNV2 (CNVer) #8

Closed GoogleCodeExporter closed 9 years ago

GoogleCodeExporter commented 9 years ago 

Hi Ivo,

I have connected the CNVer step to the script. When I validate I have this 
strange message about the output and a path that is clearly on cranium. I 
searched how to change it, but I didn;t fin this output parameter in the data 
source...what does it mean?

Federica

Original issue reported on code.google.com by federica...@gmail.com on 20 Jul 2011 at 11:00

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GoogleCodeExporter commented 9 years ago 
..here the workflow

Original comment by federica...@gmail.com on 20 Jul 2011 at 11:06

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GoogleCodeExporter commented 9 years ago 
Yes, I see - there are some remnants from LONI cranium/ifs that are still left 
in the *.pipe workflow from the conversion from LONI to UCI. This automatic 
reconfiguration will be resolved perhaps in Pipeline V.5.3 (sorry!), but for 
now, you could:

(1) either open the *.pipe file using any text editor and replace the /ifs 
references with the appropriate /project* references on UCI fgene. For example:
:" 
location="pipeline://fgene3.bic.uci.edu//ifs/ccb/agenco/bioinformatics/scripts/U
CI/CNV_bowtie-build.sh"

(2) Or just in the Pipeline GUI canvas (for each module, E.g., Bowtie) you go 
to the module definition and the "Execution" tab needs to be changes to point 
to the UCI/fgene location of this executable script. For example, the Bowtie 
executable location says:
/ifs/ccb/agenco/bioinformatics/scripts/UCI/CNV_bowtie-build.sh, but should be 
something like:
/project1/*/scripts/CNV_bowtie-build.sh

Original comment by iwaterp...@gmail.com on 20 Jul 2011 at 11:38

GoogleCodeExporter commented 9 years ago 
Ivo,

Ivo I think that I have already done the (2) for each module. The errors piint 
somehow to something related to the                          output parameter 
that i cannot find. The modules are ok and directed to fgene.

Cheers,

fed

Original comment by federica...@gmail.com on 21 Jul 2011 at 12:26

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GoogleCodeExporter commented 9 years ago 
CNV2 (CNVer, see issue#8):

So, for CNV2 (CNVer): we overcame the problem described in the issue#8. The 
module ran, but I have an error in the CNVer module. No error stream, but if I 
take the command line this is what I get:

/projects1/test_pipeline/NEW_ORGANIZATION/scripts/cnver.sh --map_list 
/usr/pl_cache/pipeline/2011August04_16h02m36s134ms/MakeaList_1.OutputList-1.txt 
--ref_folder /applications/CNVer/cnver-0.8.1/hg18comp --work_dir 
/ifs/tmp/agenco/CNV --read_len 101 --mean_insert 175 --stdev_insert 25 
--min_mps 3
mkdir /ifs: Permission denied at /applications/CNVer/cnver-0.8.1/src/cnver.pl 
line 100

..the line 100 is here:

my $CNVER_FOLDER=$ENV{"CNVER_FOLDER"};
defined($CNVER_FOLDER) or die ("Error: please set CNVER_FOLDER enviornment 
variable to the correct path");

Line 100: mkpath($temp_folder);

Do you think is always a permission issue?

Original comment by federica...@gmail.com on 4 Aug 2011 at 11:09

GoogleCodeExporter commented 9 years ago 
Hi, After I have updated the pipeline version (with the one available on the 
website) I re-run the CNV2 module attached, but I have back the same error (see 
previous message:

mkdir /ifs: Permission denied at /applications/CNVer/cnver-0.8.1/src/cnver.pl 
line 100

Fed

Original comment by federica...@gmail.com on 15 Aug 2011 at 7:52