Hi everybody,
I would like to install Bio-SamTools 1.41 without root-permissions. I tried the following commands:
But I received the following error:
I tested already with different samtools versions (1.2, 0.1.17, 0.1.18). I would be happy about any suggestions. Does anybody have an idea?
Best
Robby
I would like to install Bio-SamTools 1.41 without root-permissions. I tried the following commands:
Code:
perl Build.PL --install_base /home/$User/perl5 ./Build
Code:
Building Bio-SamTools which: no nmake in ([...]) gcc -g -Wall -O2 -fPIC -o bam2bedgraph bam2bedgraph.o -L/path/samtools -lbam -lpthread -lm -lz bam2bedgraph.o: In function `main': /path/Bio-SamTools-1.41/c_bin/bam2bedgraph.c:62: undefined reference to `hts_idx_load' bam2bedgraph.o: In function `bam_index_destroy': /path/samtools/bam.h:449: undefined reference to `hts_idx_destroy' /path/samtools/libbam.a(bam_aux.o): In function `bam_parse_region': /path/samtools/bam_aux.c:63: undefined reference to `hts_parse_reg' /path/samtools/bam_aux.c:67: undefined reference to `bam_name2id' /path/samtools/libbam.a(bam.o): In function `bam_fetch': /path/software/samtools/bam.c:84: undefined reference to `bam_init1' /path/samtools/libbam.a(bam.o): In function `bam_iter_query': /path/samtools/bam.h:475: undefined reference to `sam_itr_queryi' /path/samtools/libbam.a(bam.o): In function `bam_iter_read': /path/samtools/bam.h:476: undefined reference to `hts_itr_next' /path/samtools/bam.h:476: undefined reference to `bam_read1' /path/samtools/libbam.a(bam.o): In function `bam_iter_destroy': /path/samtools/bam.h:477: undefined reference to `hts_itr_destroy' /path/samtools/libbam.a(bam.o): In function `bam_fetch': /path/samtools/bam.c:88: undefined reference to `bam_destroy1' /path/samtools/libbam.a(bam.o): In function `bam_format1': /path/samtools/bam.c:37: undefined reference to `sam_format1' /path/samtools/libbam.a(sam.o): In function `samfaipath': /path/samtools/sam.c:102: undefined reference to `hts_verbose' /path/samtools/sam.c:103: undefined reference to `fai_build' /path/samtools/libbam.a(sam.o): In function `sampileup': /path/samtools/sam.c:77: undefined reference to `bam_init1' /path/samtools/libbam.a(sam.o): In function `samread': /path/samtools/sam.h:95: undefined reference to `sam_read1' /path/samtools/libbam.a(sam.o): In function `sampileup': /path/samtools/sam.c:88: undefined reference to `bam_destroy1' /path/samtools/libbam.a(sam.o): In function `samclose': /path/samtools/sam.c:66: undefined reference to `bam_hdr_destroy' /path/samtools/sam.c:67: undefined reference to `hts_close' /path/samtools/libbam.a(sam.o): In function `samopen': /path/samtools/sam.c:41: undefined reference to `hts_open' /path/samtools/sam.c:48: undefined reference to `hts_set_fai_filename' /path/samtools/sam.c:49: undefined reference to `sam_hdr_read' /path/samtools/sam.c:51: undefined reference to `hts_verbose' /path/samtools/sam.c:57: undefined reference to `hts_get_format' /path/samtools/sam.c:57: undefined reference to `sam_hdr_write' /path/samtools/libbam.a(sam.o): In function `samthreads': /path/samtools/sam.c:33: undefined reference to `hts_get_format' /path/samtools/sam.c:34: undefined reference to `bgzf_mt' /path/samtools/libbam.a(bam_plbuf.o): In function `bam_plbuf_push': /path/samtools/bam_plbuf.c:61: undefined reference to `bam_plp_push' /path/samtools/bam_plbuf.c:63: undefined reference to `bam_plp_next' /path/samtools/libbam.a(bam_plbuf.o): In function `bam_plbuf_destroy': /path/samtools/bam_plbuf.c:53: undefined reference to `bam_plp_destroy' /path/samtools/libbam.a(bam_plbuf.o): In function `bam_plbuf_init': /path/samtools/bam_plbuf.c:45: undefined reference to `bam_plp_init' /path/samtools/libbam.a(bam_plbuf.o): In function `bam_plbuf_reset': /path/samtools/bam_plbuf.c:38: undefined reference to `bam_plp_reset' collect2: ld returned 1 exit status make: *** [bam2bedgraph] Error 1
Best
Robby
Comment