install-consed

[root@genomes consed-19]# mkdir /share/apps/genome/bin
[root@genomes consed-19]# cp consed_linux
consed_linux32bit consed_linux64bit consed_linux_itanium
consed_linux32bit_dyn consed_linux64bit_static consed_linux.tar.gz
[root@genomes consed-19]# cp consed_linux64bit /share/apps/genome/bin/
[root@genomes consed-19]# chmod 111 /share/apps/genome/bin/consed_linux64bit
[root@genomes consed-19]# ln -s /share/apps/genome/bin/consed_linux64bit /share/apps/genome/bin/consed
[root@genomes consed-19]# mkdir /share/apps/genome/test
[root@genomes consed-19]# cp -pr 454_newbler align454reads align454reads_answer
assembly_view autofinish solexa_example solexa_example_answer polyphred standard
selectRegions selectRegionsAnswer /share/apps/genome/test
sc]# cd misc/phd2fasta/
[root@genomes phd2fasta]# make
cp phd2fasta /share/apps/genome/bin
[root@genomes phd2fasta]# chmod 111 /share/apps/genome/bin/phd2fasta
sta]# cd ../mktrace
[root@genomes mktrace]# ls
freeTrace.c Makefile mktrace.o rwUtil.c typeDef.h
freeTrace.o mktrace readFASTA.c rwUtil.h writePhd.c
getTime.c mktrace.c readFASTA.o rwUtil.o writePhd.o
getTime.o MKTRACE.DOC readQUAL.c synTrace.c writeSCF.c
INSTALL mktrace.h readQUAL.o synTrace.o writeSCF.o
[root@genomes mktrace]# make
make: `mktrace' is up to date.
[root@genomes mktrace]# cp mktrace /share/apps/genome/bin
[root@genomes mktrace]# chmod 111 /share/apps/genome/bin/mktrace
ace]# cd ../454
[root@genomes 454]# ls
sff2scf sff2scf.c
[root@genomes 454]# gcc -o sff2scf.c -o sff2scf
gcc: no input files
[root@genomes 454]# gcc -o sff2scf.c -o s
[root@genomes 454]# ls
sff2scf sff2scf.c
[root@genomes 454]# file *.c
sff2scf.c: ASCII C program text
[root@genomes 454]# fcc -o sff2scf sff2scf.c
-bash: fcc: command not found
[root@genomes 454]# gcc -o sff2scf sff2scf.c
[root@genomes 454]# mv sff2scf /share/apps/genome/bin
[root@genomes 454]# chmod 111 /share/apps/genome/bin/sff2scf
cd ../../scripts
chmod 555 *
cp -p * /share/apps/genome/bin
(if not already installed phredpar, then need to put phredpar.dat in /share/apps/genome/lib after making it of course)
[root@genomes scripts]# mkdir /share/apps/genome/lib/screenLibs
[root@genomes scriipts]# cd ../misc
[root@genomes misc]# cp filter454Reads.fa primerCloneScreen.seq primerSubcloneScreen.seq repeats.fasta sffLinkers.fa singleVectorForRestrictionDigest.fasta vector.seq /share/apps/genome/lib/screenLibs

For Jansen Lab Server add these to phredpar.dat

1. addtions for Jansen Lab
   "KB_3130_POP7_BDTv3.mob" terminator big-dye ABI_3700
   "KB_3730_POP7_BDTv3.mob" terminator big-dye ABI_3700
   "DT3730POP7
   Unknown macro: {BDv3}
   .mob" terminator big-dye ABI_3700