Hi guys I don't think my install of Samtools is going right.
First I don't think I have zlib and I'm not sure how to install it so that samtools will see it. I think Samtools requires zlib?
I'm under the restriction that I can only write files to /mnt/galaxyData so I can't do any system wide installs.
Here's what I tried so far. Any help is greatly appreciated.
ubuntu@ip-10-88-28-88:/mnt/galaxyData/custom$ cd downloads/
ubuntu@ip-10-88-28-88:/mnt/galaxyData/custom/downloads$ wget
http://downloads.sourceforge.net/project/samtools/samtools/0.1.9/samtools-0.1.9.tar.bz2?r=http%3A%2F%2Fsourceforge.net%2Fprojects%2Fsamtools%2Ffiles%2Fsamtools%2F0.1.9%2F&ts=1326486279&use_mirror=voxel
ubuntu@ip-10-88-28-88:/mnt/galaxyData/custom/downloads$ mv
samtools-0.1.9.tar.bz2\?r\=http\:%2F%2Fsourceforge.net%2Fprojects%2Fsamtools%2Ffiles%2Fsamtools%2F0.1.9%2F
samtools-0.1.9.tar.bz2
ubuntu@ip-10-88-28-88:/mnt/galaxyData/custom/downloads$ tar jxvf
samtools-0.1.9.tar.bz2
ubuntu@ip-10-88-28-88:/mnt/galaxyData/custom/downloads$ cd samtools-0.1.9/
ubuntu@ip-10-88-28-88:/mnt/galaxyData/custom/downloads/samtools-0.1.9$
make razip
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
-D_CURSES_LIB=1 -I. razip.c -o razip.o
razip.c: In function ‘main’:
razip.c:131:10: warning: ignoring return value of ‘write’, declared
with attribute warn_unused_result [-Wunused-result]
razip.c: In function ‘write_open’:
razip.c:32:9: warning: ignoring return value of ‘scanf’, declared with
attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
-D_CURSES_LIB=1 -I. razf.c -o razf.o
razf.c: In function ‘razf_close’:
razf.c:804:9: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
razf.c:805:9: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
razf.c:808:9: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
razf.c:810:9: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘razf_end_flush’:
razf.c:258:9: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘_razf_write’:
razf.c:201:8: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘save_zindex’:
razf.c:96:17: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
razf.c:99:8: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
razf.c:106:7: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
razf.c:107:7: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
razf.c: In function ‘razf_flush’:
razf.c:221:8: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
razf.c:234:9: warning: ignoring return value of ‘write’, declared with
attribute warn_unused_result [-Wunused-result]
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_USE_KNETFILE
-D_CURSES_LIB=1 -I. knetfile.c -o knetfile.o
knetfile.c: In function ‘khttp_connect_file’:
knetfile.c:416:2: warning: ignoring return value of ‘write’, declared
with attribute warn_unused_result [-Wunused-result]
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.c:237:2: warning: ignoring return value of ‘write’, declared
with attribute warn_unused_result [-Wunused-result]
gcc -g -Wall -O2 -o razip razf.o razip.o knetfile.o -lz
ubuntu@ip-10-88-28-88:/mnt/galaxyData/custom/downloads/samtools-0.1.9$ ls -l
total 1008
-rw-r--r-- 1 ubuntu ubuntu 916 2010-07-12 02:41 AUTHORS
-rw-r--r-- 1 ubuntu ubuntu 5226 2010-10-28 02:48 bam2bcf.c
-rw-r--r-- 1 ubuntu ubuntu 860 2010-10-28 02:48 bam2bcf.h
-rw-r--r-- 1 ubuntu ubuntu 4099 2010-07-12 02:41 bam_aux.c
-rw-r--r-- 1 ubuntu ubuntu 10665 2010-10-28 02:48 bam.c
-rw-r--r-- 1 ubuntu ubuntu 2803 2010-07-12 02:41 bam_color.c
-rw-r--r-- 1 ubuntu ubuntu 1064 2010-07-12 02:41 bam_endian.h
-rw-r--r-- 1 ubuntu ubuntu 24002 2010-10-28 02:48 bam.h
-rw-r--r-- 1 ubuntu ubuntu 14553 2010-07-12 02:41 bam_import.c
-rw-r--r-- 1 ubuntu ubuntu 20659 2010-10-28 02:48 bam_index.c
-rw-r--r-- 1 ubuntu ubuntu 4976 2010-07-12 02:41 bam_lpileup.c
-rw-r--r-- 1 ubuntu ubuntu 20595 2010-10-28 02:48 bam_maqcns.c
-rw-r--r-- 1 ubuntu ubuntu 1486 2010-10-28 02:48 bam_maqcns.h
-rw-r--r-- 1 ubuntu ubuntu 2540 2010-07-12 02:41 bam_mate.c
-rw-r--r-- 1 ubuntu ubuntu 9096 2010-10-28 02:48 bam_md.c
-rw-r--r-- 1 ubuntu ubuntu 12070 2010-10-28 02:48 bam_pileup.c
-rw-r--r-- 1 ubuntu ubuntu 28030 2010-10-28 02:48 bam_plcmd.c
-rw-r--r-- 1 ubuntu ubuntu 1465 2010-07-12 02:41 bam_reheader.c
-rw-r--r-- 1 ubuntu ubuntu 5631 2010-07-12 02:41 bam_rmdup.c
-rw-r--r-- 1 ubuntu ubuntu 4127 2010-07-12 02:41 bam_rmdupse.c
-rw-r--r-- 1 ubuntu ubuntu 12370 2010-10-28 02:48 bam_sort.c
-rw-r--r-- 1 ubuntu ubuntu 2688 2010-07-12 02:41 bam_stat.c
-rw-r--r-- 1 ubuntu ubuntu 5215 2010-10-28 02:48 bamtk.c
-rw-r--r-- 1 ubuntu ubuntu 12761 2010-10-28 02:48 bam_tview.c
drwxr-xr-x 2 ubuntu ubuntu 4096 2012-01-13 20:25 bcftools
-rw-r--r-- 1 ubuntu ubuntu 18806 2010-10-28 02:48 bgzf.c
-rw-r--r-- 1 ubuntu ubuntu 4599 2010-07-12 02:41 bgzf.h
-rw-r--r-- 1 ubuntu ubuntu 5903 2010-10-28 02:48 bgzip.c
-rw-r--r-- 1 ubuntu ubuntu 168011 2010-10-28 02:48 ChangeLog
-rw-r--r-- 1 ubuntu ubuntu 1085 2010-07-12 02:41 COPYING
-rw-r--r-- 1 ubuntu ubuntu 3485 2010-10-28 02:48 errmod.c
-rw-r--r-- 1 ubuntu ubuntu 317 2010-10-28 02:48 errmod.h
drwxr-xr-x 2 ubuntu ubuntu 130 2012-01-13 20:25 examples
-rw-r--r-- 1 ubuntu ubuntu 10271 2010-07-12 02:41 faidx.c
-rw-r--r-- 1 ubuntu ubuntu 3188 2010-07-12 02:41 faidx.h
-rw-r--r-- 1 ubuntu ubuntu 5931 2010-07-12 02:41 glf.c
-rw-r--r-- 1 ubuntu ubuntu 1799 2010-07-12 02:41 glf.h
-rw-r--r-- 1 ubuntu ubuntu 1003 2010-07-12 02:41 INSTALL
-rw-r--r-- 1 ubuntu ubuntu 19312 2010-10-28 02:48 kaln.c
-rw-r--r-- 1 ubuntu ubuntu 1974 2010-10-28 02:48 kaln.h
-rw-r--r-- 1 ubuntu ubuntu 16522 2010-07-12 02:41 khash.h
-rw-r--r-- 1 ubuntu ubuntu 3472 2010-07-12 02:41 klist.h
-rw-r--r-- 1 ubuntu ubuntu 18226 2010-07-12 02:41 knetfile.c
-rw-r--r-- 1 ubuntu ubuntu 1611 2010-07-12 02:41 knetfile.h
-rw-rw-r-- 1 ubuntu ubuntu 41368 2012-01-13 20:34 knetfile.o
-rw-r--r-- 1 ubuntu ubuntu 8108 2010-07-12 02:41 kseq.h
-rw-r--r-- 1 ubuntu ubuntu 10027 2010-10-28 02:48 ksort.h
-rw-r--r-- 1 ubuntu ubuntu 5186 2010-10-28 02:48 kstring.c
-rw-r--r-- 1 ubuntu ubuntu 2641 2010-10-28 02:48 kstring.h
-rw-r--r-- 1 ubuntu ubuntu 2670 2010-10-28 02:48 Makefile
-rw-r--r-- 1 ubuntu ubuntu 1592 2010-07-12 02:41 Makefile.mingw
drwxr-xr-x 2 ubuntu ubuntu 4096 2012-01-13 20:25 misc
-rw-r--r-- 1 ubuntu ubuntu 14319 2010-10-28 02:48 NEWS
-rw-r--r-- 1 ubuntu ubuntu 24343 2010-07-12 02:41 razf.c
-rw-r--r-- 1 ubuntu ubuntu 4137 2010-07-12 02:41 razf.h
-rw-rw-r-- 1 ubuntu ubuntu 49912 2012-01-13 20:34 razf.o
-rwxrwxr-x 1 ubuntu ubuntu 84056 2012-01-13 20:34 razip
-rw-r--r-- 1 ubuntu ubuntu 4110 2010-10-28 02:48 razip.c
-rw-rw-r-- 1 ubuntu ubuntu 36360 2012-01-13 20:34 razip.o
-rw-r--r-- 1 ubuntu ubuntu 5503 2010-07-12 02:41 sam.c
-rw-r--r-- 1 ubuntu ubuntu 2625 2010-07-12 02:41 sam.h
-rw-r--r-- 1 ubuntu ubuntu 19200 2010-07-12 02:41 sam_header.c
-rw-r--r-- 1 ubuntu ubuntu 643 2010-07-12 02:41 sam_header.h
-rw-r--r-- 1 ubuntu ubuntu 2500 2010-10-28 02:48 sample.c
-rw-r--r-- 1 ubuntu ubuntu 396 2010-10-28 02:48 sample.h
-rw-r--r-- 1 ubuntu ubuntu 18877 2010-10-28 02:48 samtools.1
-rw-r--r-- 1 ubuntu ubuntu 25286 2010-10-28 02:48 samtools.txt
-rw-r--r-- 1 ubuntu ubuntu 9526 2010-10-28 02:48 sam_view.c
drwxr-xr-x 2 ubuntu ubuntu 49 2010-07-12 02:41 win32
