1#!/bin/csh
2
3# for running under cygwin
4
5# with EMBOSS under ~/devemboss
6
7# and emboss-ms under ~/emboss-ms
8# cd ~/
9
10# save data files
11
12setenv EMBOSS_DATA ~/devemboss/emboss/data
13
14cd ~/datafiles
15
16echo "Updating datafiles from ~/datafiles/*"
17
18echo "AAINDEX (nakai)"
19rm ~/devemboss/emboss/data/AAINDEX/[a-z]*[0-9]
20aaindexextract nakai/aaindex1 -auto
21
22echo "JASPAR"
23rm -rf ~/devemboss/emboss/data/JASPAR_*/*.pfm
24rm -rf ~/devemboss/emboss/data/JASPAR_*/matrix_list.txt
25jaspextract jaspar/all_data/FlatFileDir -auto
26
27echo "PRINTS"
28rm ~/devemboss/emboss/data/PRINTS/PR*
29rm ~/devemboss/emboss/data/PRINTS/prints.mat
30printsextract prints/prints[0-9]*.dat -auto
31
32echo "PROSITE"
33rm ~/devemboss/emboss/data/PROSITE/PS*
34rm ~/devemboss/emboss/data/PROSITE/prosite.lines
35prosextract prosite -auto
36
37echo "REBASE"
38rm ~/devemboss/emboss/data/REBASE/emboss*.*
39rebaseextract rebase/withrefm.[0-9]* rebase/proto.[0-9]* -auto
40
41echo "TRANSFAC"
42rm ~/devemboss/emboss/data/tf*
43tfextract transfac/site.dat -auto
44
45cd ~/devemboss/scripts
46
47# make sure protection is set correctly on external .exe files
48
49chmod ugo+x ~/devemboss/win32/exes/*.exe
50
51# compile the bundlewin executable
52
53gcc -o bundlewin -O2 bundlewin.c
54
55# set the default location of Visual C++ libraries
56
57setenv vc100files /home/emboss/emboss-ms/redist/vc100
58setenv vc90files /home/emboss/emboss-ms/redist/vc90
59setenv vc80files /home/emboss/emboss-ms/redist/vc80
60
61if(-d ~/membossdev/win32build) then
62  rm -rf ~/membossdev/win32build
63endif
64
65if (-s ~/membossdev/memboss-dev.zip) then
66  rm ~/membossdev/memboss-dev.zip
67endif
68
69# run and accept default (see above) VC++ library locations
70
71./bundlewin /home/emboss/devemboss /home/emboss/membossdev
72
73echo "when ready, unpack with"
74echo "cd ~/membossdev"
75echo "rename or remove memboss-dev directory"
76echo "unzip -q ~/membossdev/memboss-dev.zip"
77echo "or unzip in windows by opening the memboss-dev.zip file"
78