Dear EMBOSS programmers, I am using EMBOSS in a context where I can not expect $HOME to be set. Therefore, I created a .embossrc from a template and attempted to use it in the current directory. However, EMBOSS does not seem to read it, despite what is written in the documentation:
http://emboss.sourceforge.net/docs/adminguide/node4.html Here is an example: # The template: sorbet【tmp】$ cat mirbase.embossrc DB mirbase [ type: N format: embl method: emblcd directory: /usr/share/mirbase/emboss file: *.dat ] # Creation of the .embossrc: sorbet【tmp】$ PWD=`pwd` perl -pe "s(/usr/share/mirbase/emboss)($PWD)" < mirbase.embossrc | tee .embossrc DB mirbase [ type: N format: embl method: emblcd directory: /home/charles/tmp file: *.dat ] # It does not work, but the .embossrc is functional in $HOME sorbet【tmp】$ seqret mirbase:MI0000007 stdout Reads and writes (returns) sequences Error: Failed to open filename 'mirbase' Error: Unable to read sequence 'mirbase:MI0000007' Died: seqret terminated: Bad value for '-sequence' and no prompt sorbet【tmp】$ cp .embossrc $HOME sorbet【tmp】$ seqret mirbase:MI0000007 stdout Reads and writes (returns) sequences >cel-mir-36 MI0000007 Caenorhabditis elegans miR-36 stem-loop caccgcugucggggaaccgcgccaauuuucgcuucagugcuagaccauccaaagugucua ucaccgggugaaaauucgcauggguccccgacgcgga # Strace confirms that the current dir is not searched for .embossrc sorbet【tmp】$ rm $HOME/.embossrc sorbet【tmp】$ strace seqret mirbase:MI0000007 stdout 2>&1 | grep embossrc open("/home/charles/.embossrc", O_RDONLY|O_LARGEFILE) = -1 ENOENT (No such file or directory) sorbet【tmp】$ strace seqret mirbase:MI0000007 stdout 2>&1 | grep emboss.default open("/usr/share/EMBOSS/emboss.default", O_RDONLY|O_LARGEFILE) = -1 ENOENT (No such file or directory) open("/home/charles/debian/EMBOSS-4.1.0/emboss/emboss.default", O_RDONLY|O_LARGEFILE) = -1 ENOENT (No such file or directory) Interestingly, it searches also emboss.default in a place which is not expected: where I compiled EMBOSS... Can I have made a mistake at compilation time which would prevent `pwd`/.embossrc to be parsed? Have a nice day, -- Charles Plessy Debian-Med packaging team http://www.debian.org/devel/debian-med/ Wako, Saitama, Japan _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
