155 lines
5.2 KiB
Bash
155 lines
5.2 KiB
Bash
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#!/bin/csh -f
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# This file must be sourced after, or at the end of, staden.login
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# It sets up the sequence libraries for use by the software
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# Edit this file to set environment variables for the paths to the homes of
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# your sequence libraries and their associated files
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#
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# First choose a home for the library data - ie the division files, and the
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# index files. Then set up the paths in this file.
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#
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#####################################################################################
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#
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# Introduction
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# ------------
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# The sequence libraries are made available to the programs by several levels
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# of files. At the top of the tree is a file that says which libraries are
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# available locally and defines environment variables to point to the next
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# level of files. It also tells the programs (with its library type flag) the
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# format of the library (embl, embl-updates and swissprot are of library type A;
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# PIR, NRL3D are of type B and Genbank type C).
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# The file is called sequence.libs and is distributed in $STADTABL and is given
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# the environment variable SEQUENCELIBRARIES which is defined in this file.
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# setenv SEQUENCELIBRARIES $STADTABL/sequence.libs
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# Contents of file sequence.libs
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#A EMBLFILES EMBL 30 nucleotide library Dec 91! in cdrom format
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#A EMBLUFILES EMBL 30 updates library Dec 91! in cdrom format
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#A SWISSFILES SWISSPROT 20 protein library Nov 91! in cdrom format
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#B PIRFILES PIR 31 protein library Dec 91!
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#B NRL3DFILES NRL3D 58 From Brookhaven protein library Dec 91!
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#C GENBFILES GenBank example!
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#! format is: library type, space, name of library description file, prompt
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#! anything after ! is ignored
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# end of file
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# For example the first line defines a library of type A, and environment variable
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# (see below) EMBLFILES, and the text "EMBL 30 nucleotide library Dec 91" would
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# appear on the users screen.
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# Four environment variables are required to define each library so that it can
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# be used by the software:
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# 1. The first to a file that contains a list of the files (such as indexes)
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# used by the programs.
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# 2. A path to the directory that contains the division_lookup file.
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# 3. A path to the directory that contains the index files.
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# 4. A path to the directory that contains the division (or data) files.
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# For example, for EMBL
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# setenv EMBLFILES $STADTABL/embl.files
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# setenv EMBLDIVPATH /nfs/al/pubseq/pubseq/inhouse/al-generic/tables
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# setenv EMBLINDPATH /nfs/al/pubseq/pubseq/seqlibs/embl
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# setenv EMBLPATH /nfs/al/pubseq/pubseq/seqlibs/embl
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# (Of course the division_lookup, indexes and data files could be in the same place)
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# Making a new library available to the programs
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# ----------------------------------------------
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#
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# If making (say) embl available to the programs for the first time you would need
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# to add a line to the file $STADTABL/sequence.libs (embl, embl-updates and
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# swissprot are of library type A; PIR, NRL3D are of type B and Genbank type C),
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# and you would need to define EMBLPATH and EMBLINDPATH. No other changes should
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# be required.
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# Moving the location of indexes or data files
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# --------------------------------------------
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# If you move the data files for embl you need to redefine EMBLPATH.
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# If you move the index files for embl you would need to redefine EMBLINDPATH.
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# The other files (on the distribution tape stored in $STADTABL) will only
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# require changes if the libraries are reorganised - eg when embl added two
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# extra divisions in spring 1993 the division lookup file needed changing.
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#
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# End of introdiction
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# -------------------
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#####################################################################################
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#
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#
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# First define the file containing the names and environment variables
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# for the locally available libraries.
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#
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setenv SEQUENCELIBRARIES $STADTABL/sequence.libs
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# Now do the individual libraries
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#
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# EMBL library
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#
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setenv EMBLFILES $STADTABL/embl.files
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setenv EMBLDIVPATH /nfs/al/pubseq/pubseq/inhouse/al-generic/tables
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setenv EMBLPATH /nfs/al/pubseq/pubseq/seqlibs/embl
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setenv EMBLINDPATH /nfs/al/pubseq/pubseq/seqlibs/embl
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#
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# EMBL updates library
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#
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setenv EMBLUFILES $STADTABL/emblu.files
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setenv EMBLUDIVPATH /nfs/al/pubseq/pubseq/inhouse/al-generic/tables
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setenv EMBLUPATH /nfs/al/pubseq/pubseq/seqlibs/embl-updates
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setenv EMBLUINDPATH /nfs/al/pubseq/pubseq/seqlibs/embl-updates
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#
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# SWISSPROT library
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#
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setenv SWISSFILES $STADTABL/swiss.files
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setenv SWISSDIVPATH /nfs/al/pubseq/pubseq/inhouse/al-generic/tables
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setenv SWISSPATH /nfs/al/pubseq/pubseq/seqlibs/swiss
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setenv SWISSINDPATH /nfs/al/pubseq/pubseq/seqlibs/swiss
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#
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# PIR library
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#
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setenv PIRFILES $STADTABL/pir.files
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setenv PIRDIVPATH /nfs/al/pubseq/pubseq/inhouse/al-generic/tables
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setenv PIRPATH /nfs/al/pubseq/pubseq/seqlibs/pir
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setenv PIRINDPATH /nfs/al/pubseq/pubseq/seqlibs/pir
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#
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# GenBank library
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#
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setenv GENBFILES $STADTABL/genbank.files
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setenv GENBDIVPATH /nfs/al/pubseq/pubseq/inhouse/al-generic/tables
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setenv GENBPATH /nfs/al/pubseq/pubseq/seqlibs/genbank
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setenv GENBINDPATH /nfs/al/pubseq/pubseq/seqlibs/genbank
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#
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# NRL3D library
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#
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setenv NRL3DFILES $STADTABL/nrl3d.files
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setenv NRL3DDIVPATH /nfs/al/pubseq/pubseq/inhouse/al-generic/tables
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setenv NRL3DPATH /nfs/al/pubseq/pubseq/seqlibs/pir
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setenv NRL3DINDPATH /nfs/al/pubseq/pubseq/seqlibs/pir
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