[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 # 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{BDv3}.mob" terminator big-dye ABI_3700 |