Q:
I tried to run the software PseudoPipe
(http://pseudogene.org/DOWNLOADS/pipeline_codes/ppipe.tar.gz) using the
example as following:
./pseudopipe.sh ~/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a
~/bin/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/dna_rm.fa
/home/liuhui/bin/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/dna/Caenorhabditis_elegans.WS220.62.dna.chromosome.%s.fa
~/bin/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/pep/Caenorhabditis_elegans.WS220.62.pep.fa
/home/liuhui/bin/pgenes/ppipe_input/caenorhabditis_elegans_62_220a/mysql/chr%s_exLocs
0

And I got the output in the attachment and attfollowing lines in the screen:
Making directories
Copying sequences
Fomatting the DNAs
Preparing the blast jobs
Finished blast
Processing blast output
Finished processing blast output
Running Pseudopipe on both strands
Working on M strand
sh: 1: source: Permission denied
Finished Pseudopipe on strand M
Working on P strand
sh: 1: source: Permission denied
Finished Pseudopipe on strand P
Generating final results
find:
`/home/liuhui/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/minus/pgenes’:
No such file or directory
find:
`/home/liuhui/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/plus/pgenes’:
No such file or directory
gzip:
/home/liuhui/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/*/pgenes/*.all.fa:
No such file or directory
Finished generating pgene full alignment
Finished running Pseudopipe

Could you please help me in solving the problem?

A:
Looks like you have permission problems. The script tries to source the file setenvPipelineVars that you will find in /home/liuhui/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/minus and /home/liuhui/bin/pgenes/ppipe_output/caenorhabditis_elegans_62_220a/pgenes/plus . If you open that file you’ll see a couple of export functions and from the look of it I would guess that you do not have rights to export to the Path. So I suggest you get admin rights and run as root.