On 05/14/12 20:41, Hermann Norpois wrote:
To whom it may conern.
I have problems to install the jaspar database. My emboss database
directory is /usr/share/EMBOSS/data. The jaspar files are dummies. This is
okay.
I downloaded Archive.zip from the jaspar site, extracted it to ~/jaspar and
got 3 directories:
drwxr-xr-x 5 hnorpois hnorpois 4096 2012-05-14 21:04 all_data
drwxr-xr-x 10 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_collections
drwxr-xr-x 4 hnorpois hnorpois 4096 2012-05-14 21:04 jaspar_CORE
Now i started from the command line
jaspextract
and get
Extract data from JASPAR
JASPAR database directory [.]:
I do not understand what to type after JASPAR database directory [.]:
I tried all variations I can imagine (e.g.: ~/jaspar, ~/jaspar/all_data,
~/jaspar/all_data/FlatFileDir) but I always get the answer:
Error: Unable to open directory '~/jaspar/'
Could anybody give me an instruction?
The help (jaspextract -help) has a clue. The directory is 'The
FlatFileDir directory containing the .pfm files and the matrix_list.txt
file' so if you are in the jaspar directory you could reply with
all_data/FlatFileDir/
You are being (reasonably) confused because EMBOSS is not interpreting
the '~' in your response. That is an omission by us ... it will fill in
the directory when it sees '~' for an input file, but not for an input
directory. This will be fixed in the next release. Meanwhile a full or
relative path will be fine.
Hope this helps,
Peter Rice
EMBOSS Team
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