TR: Seqret does not work in a crontab
Johanne.Duhaime at ircm.qc.ca
Fri Mar 14 20:14:59 UTC 2003
Thank you everyone for answers.
The problem was solved by putting .embossrc in the $HOME of the user.
I have a perl program that use "seqret" to retrieve a list of sequences (and do other things).
The target command used is:
seqret -sequence=@/seqdata/seqdatabases/protein_embl/mammalian/mammalian.id -outseq=/seqdata/seqdatabases/protein_embl/mammalian/mammalian.dat -osformat=SWISS
The file /seqdata/seqdatabases/protein_embl/mammalian/mammalian.id contains names of sequenes like:
and prot is define in .embossrc
This program works fine on the command line call. The problem arises when I put that program in a crontab. Then I have the following:
Reads and writes (returns) sequences
Error: failed to open filename prot
Error: Unable to read sequence '@/seqdata/seqdatabases/protein_embl/mammalian/mammalian.id'
It looks like it could recognize "prot".
Can you help me?
More information about the EMBOSS