Hi everyone,
Can anyone show me how to install samtools step by step?
I hope someone answers this naive question::
best,
Can anyone show me how to install samtools step by step?
I hope someone answers this naive question::
best,
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[COLOR="Red"]vo-zapus:/windows/D/samtools # make make[1]: Entering directory `/windows/D/samtools' make[2]: Entering directory `/windows/D/samtools' make[2]: Nothing to be done for `lib'. make[2]: Leaving directory `/windows/D/samtools' make[2]: Entering directory `/windows/D/samtools/bcftools' make[2]: Nothing to be done for `lib'. make[2]: Leaving directory `/windows/D/samtools/bcftools' make[2]: Entering directory `/windows/D/samtools/misc' make[2]: Nothing to be done for `lib'. make[2]: Leaving directory `/windows/D/samtools/misc' gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -D_CURSES_LIB=1 -I. bam_tview.c -o bam_tview.o make[1]: gcc: Command not found make[1]: *** [bam_tview.o] Error 127 make[1]: Leaving directory `/windows/D/samtools' make: *** [all-recur] Error 1[/COLOR]
[COLOR="Red"]evo-zapus:/windows/D/pysqlite # python setup.py build running build running build_py creating build creating build/lib.linux-x86_64-2.7 creating build/lib.linux-x86_64-2.7/pysqlite2 copying lib/dbapi2.py -> build/lib.linux-x86_64-2.7/pysqlite2 copying lib/dump.py -> build/lib.linux-x86_64-2.7/pysqlite2 copying lib/__init__.py -> build/lib.linux-x86_64-2.7/pysqlite2 creating build/lib.linux-x86_64-2.7/pysqlite2/test copying lib/test/dbapi.py -> build/lib.linux-x86_64-2.7/pysqlite2/test copying lib/test/dump.py -> build/lib.linux-x86_64-2.7/pysqlite2/test copying lib/test/factory.py -> build/lib.linux-x86_64-2.7/pysqlite2/test copying lib/test/hooks.py -> build/lib.linux-x86_64-2.7/pysqlite2/test copying lib/test/py25tests.py -> build/lib.linux-x86_64-2.7/pysqlite2/test copying lib/test/regression.py -> build/lib.linux-x86_64-2.7/pysqlite2/test copying lib/test/transactions.py -> build/lib.linux-x86_64-2.7/pysqlite2/test copying lib/test/types.py -> build/lib.linux-x86_64-2.7/pysqlite2/test copying lib/test/userfunctions.py -> build/lib.linux-x86_64-2.7/pysqlite2/test copying lib/test/__init__.py -> build/lib.linux-x86_64-2.7/pysqlite2/test running build_ext building 'pysqlite2._sqlite' extension creating build/temp.linux-x86_64-2.7 creating build/temp.linux-x86_64-2.7/src gcc -pthread -fno-strict-aliasing -g -O2 -DNDEBUG -fmessage-length=0 -O2 -Wall -D_FORTIFY_SOURCE=2 -fstack-protector -funwind-tables -fasynchronous-unwind-tables -g -fPIC -DMODULE_NAME="pysqlite2.dbapi2" -DSQLITE_OMIT_LOAD_EXTENSION=1 -I/usr/include/python2.7 -c src/module.c -o build/temp.linux-x86_64-2.7/src/module.o unable to execute gcc: No such file or directory error: command 'gcc' failed with exit status 1[/COLOR]
akram@evo-zapus /cygdrive/c/samtools-0.1.9 $ make make[1]: Entering directory `/cygdrive/c/samtools-0.1.9' make[2]: Entering directory `/cygdrive/c/samtools-0.1.9' make[2]: Nothing to be done for `lib'. make[2]: Leaving directory `/cygdrive/c/samtools-0.1.9' make[2]: Entering directory `/cygdrive/c/samtools-0.1.9/bcftools' make[2]: Nothing to be done for `lib'. make[2]: Leaving directory `/cygdrive/c/samtools-0.1.9/bcftools' make[2]: Entering directory `/cygdrive/c/samtools-0.1.9/misc' make[2]: Nothing to be done for `lib'. make[2]: Leaving directory `/cygdrive/c/samtools-0.1.9/misc' gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_tview.c -o bam_tview.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_maqcns.c -o bam_maqcns.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_plcmd.c -o bam_plcmd.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. sam_view.c -o sam_view.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_rmdup.c -o bam_rmdup.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_rmdupse.c -o bam_rmdupse.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_mate.c -o bam_mate.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_stat.c -o bam_stat.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam_color.c -o bam_color.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bamtk.c -o bamtk.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. kaln.c -o kaln.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. bam2bcf.c -o bam2bcf.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. errmod.c -o errmod.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I. sample.c -o sample.o gcc -I/usr/include/ncurses -o samtools bam_tview.o bam_maqcns.o bam_plcmd.o sam_view.o bam_rmdup.o bam_rmdupse.o bam_mate.o bam_stat.o bam_color.o bamtk.o kaln.o bam2bcf.o errmod.o sample.o libbam.a -lm -lcurses -lz -Lbcftools -lbcf make[1]: Leaving directory `/cygdrive/c/samtools-0.1.9' make[1]: Entering directory `/cygdrive/c/samtools-0.1.9/bcftools' gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I.. -I. call1.c -o call1.o gcc -c -I/usr/include/ncurses -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE -D_CURSES_LIB=1 -Dexpl=exp -Dlogl=log -I.. -I. main.c -o main.o gcc -I/usr/include/ncurses -o bcftools call1.o main.o ../kstring.o ../bgzf.o ../knetfile.o -lm -lz -L. -lbcf ./libbcf.a(prob1.o): In function `mc_cal_y': /cygdrive/c/samtools-0.1.9/bcftools/prob1.c:275: undefined reference to `_expl' collect2: ld returned 1 exit status Makefile:34: recipe for target `bcftools' failed make[1]: *** [bcftools] Error 1 make[1]: Leaving directory `/cygdrive/c/samtools-0.1.9/bcftools' Makefile:26: recipe for target `all-recur' failed make: *** [all-recur] Error 1
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