Install dwgsim problem - location of samtools binaries error

[shangjin]

How I fixed it... Basically it was that the sym-link to the binaries folder had to be in the root of the dwgsim folder to allow it to compile. Once that was done, the samtools binaries can be deleted.

I also have a similar problems with yours.
I renamed samtools-1.2 as samtools, and placed it in the root of the dwgsim folder. Then I type make. But I got this error.

make[1]: Entering directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
gcc -g -Wall -O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION="0.1.11" -I. -c -o bam_index.o bam_index.c
bam_index.c:27:24: error: htslib/hts.h: No such file or directory
bam_index.c:28:24: error: htslib/sam.h: No such file or directory
bam_index.c:29:26: error: htslib/khash.h: No such file or directory
bam_index.c: In function ‘bam_index’:
bam_index.c:75: warning: implicit declaration of function ‘bam_index_build’
bam_index.c: In function ‘bam_idxstats’:
bam_index.c:81: error: ‘hts_idx_t’ undeclared (first use in this function)
bam_index.c:81: error: (Each undeclared identifier is reported only once
bam_index.c:81: error: for each function it appears in.)
bam_index.c:81: error: ‘idx’ undeclared (first use in this function)
bam_index.c:82: error: ‘bam_hdr_t’ undeclared (first use in this function)
bam_index.c:82: error: ‘header’ undeclared (first use in this function)
bam_index.c:83: error: ‘samFile’ undeclared (first use in this function)
bam_index.c:83: error: ‘fp’ undeclared (first use in this function)
bam_index.c:89: warning: implicit declaration of function ‘sam_open’
bam_index.c:91: warning: implicit declaration of function ‘sam_hdr_read’
bam_index.c:92: warning: implicit declaration of function ‘sam_index_load’
bam_index.c:101: warning: implicit declaration of function ‘hts_idx_get_stat’
bam_index.c:105: warning: implicit declaration of function ‘hts_idx_get_n_no_coor’
bam_index.c:106: warning: implicit declaration of function ‘bam_hdr_destroy’
bam_index.c:107: warning: implicit declaration of function ‘hts_idx_destroy’
bam_index.c:108: warning: implicit declaration of function ‘sam_close’
make[1]: *** [bam_index.o] Error 1
make[1]: Leaving directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
make: *** [all-recur] Error 1
[root@localhost dwgsim]# make clean
make[1]: Entering directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
make[1]: *** No rule to make target `cleanlocal'. Stop.
make[1]: Leaving directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
make: *** [cleanlocal-recur] Error 1
[root@localhost dwgsim]# make
make[1]: Entering directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
gcc -g -Wall -O3 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_USE_KNETFILE -DPACKAGE_VERSION="0.1.11" -I. -c -o bam_index.o bam_index.c
bam_index.c:27:24: error: htslib/hts.h: No such file or directory
bam_index.c:28:24: error: htslib/sam.h: No such file or directory
bam_index.c:29:26: error: htslib/khash.h: No such file or directory
bam_index.c: In function ‘bam_index’:
bam_index.c:75: warning: implicit declaration of function ‘bam_index_build’
bam_index.c: In function ‘bam_idxstats’:
bam_index.c:81: error: ‘hts_idx_t’ undeclared (first use in this function)
bam_index.c:81: error: (Each undeclared identifier is reported only once
bam_index.c:81: error: for each function it appears in.)
bam_index.c:81: error: ‘idx’ undeclared (first use in this function)
bam_index.c:82: error: ‘bam_hdr_t’ undeclared (first use in this function)
bam_index.c:82: error: ‘header’ undeclared (first use in this function)
bam_index.c:83: error: ‘samFile’ undeclared (first use in this function)
bam_index.c:83: error: ‘fp’ undeclared (first use in this function)
bam_index.c:89: warning: implicit declaration of function ‘sam_open’
bam_index.c:91: warning: implicit declaration of function ‘sam_hdr_read’
bam_index.c:92: warning: implicit declaration of function ‘sam_index_load’
bam_index.c:101: warning: implicit declaration of function ‘hts_idx_get_stat’
bam_index.c:105: warning: implicit declaration of function ‘hts_idx_get_n_no_coor’
bam_index.c:106: warning: implicit declaration of function ‘bam_hdr_destroy’
bam_index.c:107: warning: implicit declaration of function ‘hts_idx_destroy’
bam_index.c:108: warning: implicit declaration of function ‘sam_close’
make[1]: *** [bam_index.o] Error 1
make[1]: Leaving directory `/newdisk/genome/velvet_1.2.10/MetaVelvetSLv1.0/dwgsim/samtools'
make: *** [all-recur] Error 1

###############################################
Then I checked the samtools folder. There is a folder named htslib-1.2.1. Within this folder, there a folder named htslib. The problem is that I found the files hts.h, sam.h, and khash.h. I don't understand why it reported that there are no these files.

Thank you very much for your suggestion.

[swNGS]

How I fixed it... Basically it was that the sym-link to the binaries folder had to be in the root of the dwgsim folder to allow it to compile. Once that was done, the samtools binaries can be deleted.

[nilshomer]

Try "make clean" then "make", but also read the README. If you still get a seg fault, please post a test case to [email protected]. The maintainer (me) is responsive.

[adamhfreedman]

Having fixed the samtools binaries problem on a mac (osx), and after make went w/o a hitch, getting 'Segmentation fault' when running even the most basic command line arguments.

[pythonlovesbowtie]

Most likely you need to create a symbolic link to the samtools source code, but you could post your error message or more info.

Thanks! It works now. What I did is put samtools folder in the dwgsim folder and then dwgsim was able to find what it needs. Though I still do not know what is wrong with the soft link.

The error message was:
Firstly I made the symbolic link in my home folder as an understanding of "the root directory"
~$ ln -s samtools-0.1.17 samtools
~$ cd dwgsim/
~/dwgsim$ make
cd: 8: can't cd to samtools
make[1]: Entering directory `/home/heather/dwgsim'
cd: 8: can't cd to samtools
make[2]: Entering directory `/home/heather/dwgsim'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/home/heather/dwgsim'
make[2]: Entering directory `/home/heather/dwgsim'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/home/heather/dwgsim'
gcc -g -Wall -O2 -o dwgsim src/dwgsim_opt.o src/mut.o src/contigs.o src/regions_bed.o src/mut_txt.o src/mut_bed.o src/mut_vcf.o src/mut_input.o src/dwgsim.o -lm -lz
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. src/dwgsim_eval.c -o src/dwgsim_eval.o
src/dwgsim_eval.c:10:26: fatal error: samtools/bam.h: No such file or directory
compilation terminated.
make[1]: *** [src/dwgsim_eval.o] Error 1
make[1]: Leaving directory `/home/heather/dwgsim'
make: *** [all-recur] Error 1

################################################
Then I made a link in the dwgsim folder
~$ ln -s samtools-0.1.17 dwgsim/samtools
~$ cd dwgsim/
~/dwgsim$ make
same error messages as above.
~/dwgsim$ cd samtools
bash: cd: samtools: No such file or directory
which means I cannot cd to that link so I decided to move the samtools-0.1.17 folder in and rename it to samtools, then it worked.
################################################
~$ mv samtools-0.1.17 dwgsim/samtools
~$ cd dwgsim
~/dwgsim$ make
make[1]: Entering directory `/home/heather/dwgsim/samtools'
make[2]: Entering directory `/home/heather/dwgsim/samtools'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bgzf.c -o bgzf.o
bgzf.c: In function ‘bgzf_check_EOF’:
bgzf.c:681:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. kstring.c -o kstring.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_aux.c -o bam_aux.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam.c -o bam.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_import.c -o bam_import.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. sam.c -o sam.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_index.c -o bam_index.o
bam_index.c: In function ‘bam_index_load_core’:
bam_index.c:330:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:337:7: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:350:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:353:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:357:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:361:9: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:371:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
bam_index.c:375:8: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_pileup.c -o bam_pileup.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_lpileup.c -o bam_lpileup.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_md.c -o bam_md.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. razf.c -o razf.o
razf.c: In function ‘razf_close’:
razf.c:815:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:816:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:819:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:821:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c: In function ‘razf_end_flush’:
razf.c:260:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c: In function ‘_razf_write’:
razf.c:203:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c: In function ‘save_zindex’:
razf.c:96:17: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:99:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:106:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:107:7: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c: In function ‘razf_open_r’:
razf.c:422:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
razf.c:430:7: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
razf.c: In function ‘load_zindex’:
razf.c:124:6: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
razf.c:133:6: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
razf.c:139:6: warning: ignoring return value of ‘read’, declared with attribute warn_unused_result
razf.c: In function ‘razf_flush’:
razf.c:223:8: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
razf.c:236:9: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. faidx.c -o faidx.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bedidx.c -o bedidx.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. knetfile.c -o knetfile.o
knetfile.c: In function ‘khttp_connect_file’:
knetfile.c:415:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.c:236:2: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_sort.c -o bam_sort.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. sam_header.c -o sam_header.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_reheader.c -o bam_reheader.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. kprobaln.c -o kprobaln.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I. bam_cat.c -o bam_cat.o
ar -csru libbam.a bgzf.o kstring.o bam_aux.o bam.o bam_import.o sam.o bam_index.o bam_pileup.o bam_lpileup.o bam_md.o razf.o faidx.o bedidx.o knetfile.o bam_sort.o sam_header.o bam_reheader.o kprobaln.o bam_cat.o
make[2]: Leaving directory `/home/heather/dwgsim/samtools'
make[2]: Entering directory `/home/heather/dwgsim/samtools/bcftools'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. bcf.c -o bcf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. vcf.c -o vcf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. bcfutils.c -o bcfutils.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. prob1.c -o prob1.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. em.c -o em.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. kfunc.c -o kfunc.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. kmin.c -o kmin.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. index.c -o index.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. fet.c -o fet.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. mut.c -o mut.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION="0.1.11" -I.. -I. bcf2qcall.c -o bcf2qcall.o
ar -csru libbcf.a bcf.o vcf.o bcfutils.o prob1.o em.o kfunc.o kmin.o index.o fet.o mut.o bcf2qcall.o
make[2]: Leaving directory `/home/heather/dwgsim/samtools/bcftools'
make[2]: Entering directory `/home/heather/dwgsim/samtools/misc'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/home/heather/dwgsim/samtools/misc'
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_tview.c -o bam_tview.o
bam_tview.c:434:2: warning: #warning "No curses library is available; tview is disabled."
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_plcmd.c -o bam_plcmd.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. sam_view.c -o sam_view.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_rmdup.c -o bam_rmdup.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_rmdupse.c -o bam_rmdupse.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_mate.c -o bam_mate.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_stat.c -o bam_stat.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam_color.c -o bam_color.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bamtk.c -o bamtk.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. kaln.c -o kaln.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam2bcf.c -o bam2bcf.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam2bcf_indel.c -o bam2bcf_indel.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. errmod.c -o errmod.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. sample.c -o sample.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. cut_target.c -o cut_target.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. phase.c -o phase.o
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. bam2depth.c -o bam2depth.o
gcc -g -Wall -O2 -o samtools bam_tview.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 bam2bcf_indel.o errmod.o sample.o cut_target.o phase.o bam2depth.o -Lbcftools libbam.a -lbcf -lcurses -lm -lz
make[1]: Leaving directory `/home/heather/dwgsim/samtools'
make[1]: Entering directory `/home/heather/dwgsim'
make[2]: Entering directory `/home/heather/dwgsim/samtools'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/home/heather/dwgsim/samtools'
make[2]: Entering directory `/home/heather/dwgsim'
make[2]: Nothing to be done for `lib'.
make[2]: Leaving directory `/home/heather/dwgsim'
gcc -g -Wall -O2 -o dwgsim src/dwgsim_opt.o src/mut.o src/contigs.o src/regions_bed.o src/mut_txt.o src/mut_bed.o src/mut_vcf.o src/mut_input.o src/dwgsim.o -lm -lz
gcc -c -g -Wall -O2 -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -DPACKAGE_VERSION=\"0.1.11\" -I. src/dwgsim_eval.c -o src/dwgsim_eval.o
gcc -g -Wall -O2 -o dwgsim_eval src/dwgsim_eval.o samtools/knetfile.o samtools/bgzf.o samtools/kstring.o samtools/bam_aux.o samtools/bam.o samtools/bam_import.o samtools/sam.o samtools/bam_index.o samtools/bam_pileup.o samtools/bam_lpileup.o samtools/bam_md.o samtools/razf.o samtools/faidx.o samtools/bedidx.o samtools/bam_sort.o samtools/sam_header.o samtools/bam_reheader.o samtools/kprobaln.o samtools/bam_cat.o -Lsamtools -lm -lz
make[1]: Leaving directory `/home/heather/dwgsim'

[nilshomer]

Most likely you need to create a symbolic link to the samtools source code, but you could post your error message or more info.

[pythonlovesbowtie]

Please post your answer so that others can benefit in the future.

Thanks! Actually I am dealing with exactly the same problem and looking forward to knowing how you made it.

[nilshomer]

not to worry, have sorted it out

Please post your answer so that others can benefit in the future.

[swNGS]

not to worry, have sorted it out

[swNGS]

Hi,

I have attempted (so far unsucessfully) to install dwgsim.
The installation notes suggests that there is a dependancy on the presence of samtools.
I have samtools v 0.1.18 installed to usr/local/bin

the install instructions for dwgsim:

=== Prerequisites ======= SAMtools ====SAMtools version >=0.1.7 is required. Please find SAMtoolsat http://samtools.sourceforge.net
Download the source code and place it in the root directory. After, execute the following commands:
tar -zxvf samtools-0.1.7.tar.gz
ln -s samtools-0.1.7 samtools

=== Building DWGSIM ===To build DWGSIM, execute the following commands: make

To install DWGSIM, after building, copy the following binariesto their appropriate installation directories:
dwgsim
dwgsim_eval
dwgims_pileup_eval.pl

I already have samtools installed. I understand from the above that that dwgsim needs the samtools binaries to install. I cant figure out however where to put them relative to the folder containing the source code for dwgsim, and get a fatal error: samtools/bam.h: No such file or directory

I have tried extracting the samtools binary to the root of my home directory as suggested and creating a samtools link as suggested, but the dwgsim install script cant find it.

Any suggestions would be helpful.

Thanks