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  • #1

    vcftools-0.1.14 install no bin on ubuntu 14.04

    I downloaded and unziped the master file for vcftools on github:

    ./autogen.sh
    ./configure
    make
    sudo make install

    However, I do not have a bin folder as the install stats. I do see in the src folder, in the perl folder there is a vcf.pm. Is this the path I add for perl and the cpp folder with the vcftools executable is the other path to add? Thank you .

    Code:
    cmccabe@DTV-A5211QLM:~$ cd "/home/cmccabe/Desktop/NGS/vcftools-0.1.14"
cmccabe@DTV-A5211QLM:~/Desktop/NGS/vcftools-0.1.14$ ./autogen.sh
configure.ac:16: installing './compile'
configure.ac:12: installing './install-sh'
configure.ac:12: installing './missing'
src/cpp/Makefile.am: installing './depcomp'
cmccabe@DTV-A5211QLM:~/Desktop/NGS/vcftools-0.1.14$ ./configure
checking for a BSD-compatible install... /usr/bin/install -c
checking whether build environment is sane... yes
checking for a thread-safe mkdir -p... /bin/mkdir -p
checking for gawk... gawk
checking whether make sets $(MAKE)... yes
checking whether make supports nested variables... yes
checking for g++... g++
checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ accepts -g... yes
checking for style of include used by make... GNU
checking dependency style of g++... gcc3
checking for gcc... gcc
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking whether gcc understands -c and -o together... yes
checking dependency style of gcc... gcc3
checking how to run the C preprocessor... gcc -E
checking for perl... /usr/bin/perl
checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for ZLIB... yes
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking arpa/inet.h usability... yes
checking arpa/inet.h presence... yes
checking for arpa/inet.h... yes
checking fcntl.h usability... yes
checking fcntl.h presence... yes
checking for fcntl.h... yes
checking limits.h usability... yes
checking limits.h presence... yes
checking for limits.h... yes
checking netdb.h usability... yes
checking netdb.h presence... yes
checking for netdb.h... yes
checking for stdint.h... (cached) yes
checking for stdlib.h... (cached) yes
checking for string.h... (cached) yes
checking sys/socket.h usability... yes
checking sys/socket.h presence... yes
checking for sys/socket.h... yes
checking for unistd.h... (cached) yes
checking for stdbool.h that conforms to C99... yes
checking for _Bool... yes
checking for inline... inline
checking for int16_t... yes
checking for int32_t... yes
checking for int64_t... yes
checking for int8_t... yes
checking for off_t... yes
checking for size_t... yes
checking for ssize_t... yes
checking for uint16_t... yes
checking for uint32_t... yes
checking for uint8_t... yes
checking for special C compiler options needed for large files... no
checking for _FILE_OFFSET_BITS value needed for large files... no
checking for error_at_line... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible malloc... yes
checking for stdlib.h... (cached) yes
checking for GNU libc compatible realloc... yes
checking for gethostbyaddr... yes
checking for gethostbyname... yes
checking for memset... yes
checking for pow... no
checking for select... yes
checking for socket... yes
checking for sqrt... no
checking for strchr... yes
checking for strdup... yes
checking for strerror... yes
checking for strstr... yes
checking for strtol... yes
checking that generated files are newer than configure... done
configure: creating ./config.status
config.status: creating Makefile
config.status: creating src/Makefile
config.status: creating src/cpp/Makefile
config.status: creating src/perl/Makefile
config.status: creating config.h
config.status: executing depfiles commands
cmccabe@DTV-A5211QLM:~/Desktop/NGS/vcftools-0.1.14$ make
make  all-recursive
make[1]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14'
Making all in src
make[2]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src'
Making all in cpp
make[3]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/cpp'
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-bcf_entry.o -MD -MP -MF .deps/vcftools-bcf_entry.Tpo -c -o vcftools-bcf_entry.o `test -f 'bcf_entry.cpp' || echo './'`bcf_entry.cpp
mv -f .deps/vcftools-bcf_entry.Tpo .deps/vcftools-bcf_entry.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-bcf_entry_setters.o -MD -MP -MF .deps/vcftools-bcf_entry_setters.Tpo -c -o vcftools-bcf_entry_setters.o `test -f 'bcf_entry_setters.cpp' || echo './'`bcf_entry_setters.cpp
mv -f .deps/vcftools-bcf_entry_setters.Tpo .deps/vcftools-bcf_entry_setters.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-bcf_file.o -MD -MP -MF .deps/vcftools-bcf_file.Tpo -c -o vcftools-bcf_file.o `test -f 'bcf_file.cpp' || echo './'`bcf_file.cpp
mv -f .deps/vcftools-bcf_file.Tpo .deps/vcftools-bcf_file.Po
gcc -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-bgzf.o -MD -MP -MF .deps/vcftools-bgzf.Tpo -c -o vcftools-bgzf.o `test -f 'bgzf.c' || echo './'`bgzf.c
bgzf.c: In function ‘bgzf_check_EOF’:
bgzf.c:60:39: warning: ignoring return value of ‘fread’, declared with attribute warn_unused_result [-Wunused-result]
 #define _bgzf_read(fp, buf, len) fread((buf), 1, (len), (FILE*)(fp))
                                       ^
bgzf.c:622:2: note: in expansion of macro ‘_bgzf_read’
  _bgzf_read(fp->fp, buf, 28);
  ^
mv -f .deps/vcftools-bgzf.Tpo .deps/vcftools-bgzf.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-dgeev.o -MD -MP -MF .deps/vcftools-dgeev.Tpo -c -o vcftools-dgeev.o `test -f 'dgeev.cpp' || echo './'`dgeev.cpp
mv -f .deps/vcftools-dgeev.Tpo .deps/vcftools-dgeev.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-entry.o -MD -MP -MF .deps/vcftools-entry.Tpo -c -o vcftools-entry.o `test -f 'entry.cpp' || echo './'`entry.cpp
mv -f .deps/vcftools-entry.Tpo .deps/vcftools-entry.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-entry_filters.o -MD -MP -MF .deps/vcftools-entry_filters.Tpo -c -o vcftools-entry_filters.o `test -f 'entry_filters.cpp' || echo './'`entry_filters.cpp
mv -f .deps/vcftools-entry_filters.Tpo .deps/vcftools-entry_filters.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-entry_getters.o -MD -MP -MF .deps/vcftools-entry_getters.Tpo -c -o vcftools-entry_getters.o `test -f 'entry_getters.cpp' || echo './'`entry_getters.cpp
mv -f .deps/vcftools-entry_getters.Tpo .deps/vcftools-entry_getters.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-entry_setters.o -MD -MP -MF .deps/vcftools-entry_setters.Tpo -c -o vcftools-entry_setters.o `test -f 'entry_setters.cpp' || echo './'`entry_setters.cpp
mv -f .deps/vcftools-entry_setters.Tpo .deps/vcftools-entry_setters.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-gamma.o -MD -MP -MF .deps/vcftools-gamma.Tpo -c -o vcftools-gamma.o `test -f 'gamma.cpp' || echo './'`gamma.cpp
mv -f .deps/vcftools-gamma.Tpo .deps/vcftools-gamma.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-header.o -MD -MP -MF .deps/vcftools-header.Tpo -c -o vcftools-header.o `test -f 'header.cpp' || echo './'`header.cpp
mv -f .deps/vcftools-header.Tpo .deps/vcftools-header.Po
gcc -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-knetfile.o -MD -MP -MF .deps/vcftools-knetfile.Tpo -c -o vcftools-knetfile.o `test -f 'knetfile.c' || echo './'`knetfile.c
In file included from knetfile.c:46:0:
knetfile.c: In function ‘kftp_send_cmd’:
knetfile.h:9:37: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
 #define netwrite(fd, ptr, len) write(fd, ptr, len)
                                     ^
knetfile.c:236:2: note: in expansion of macro ‘netwrite’
  netwrite(ftp->ctrl_fd, cmd, strlen(cmd));
  ^
knetfile.c: In function ‘khttp_connect_file’:
knetfile.h:9:37: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
 #define netwrite(fd, ptr, len) write(fd, ptr, len)
                                     ^
knetfile.c:415:2: note: in expansion of macro ‘netwrite’
  netwrite(fp->fd, buf, l);
  ^
mv -f .deps/vcftools-knetfile.Tpo .deps/vcftools-knetfile.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-output_log.o -MD -MP -MF .deps/vcftools-output_log.Tpo -c -o vcftools-output_log.o `test -f 'output_log.cpp' || echo './'`output_log.cpp
mv -f .deps/vcftools-output_log.Tpo .deps/vcftools-output_log.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-parameters.o -MD -MP -MF .deps/vcftools-parameters.Tpo -c -o vcftools-parameters.o `test -f 'parameters.cpp' || echo './'`parameters.cpp
mv -f .deps/vcftools-parameters.Tpo .deps/vcftools-parameters.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-variant_file.o -MD -MP -MF .deps/vcftools-variant_file.Tpo -c -o vcftools-variant_file.o `test -f 'variant_file.cpp' || echo './'`variant_file.cpp
mv -f .deps/vcftools-variant_file.Tpo .deps/vcftools-variant_file.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-variant_file_diff.o -MD -MP -MF .deps/vcftools-variant_file_diff.Tpo -c -o vcftools-variant_file_diff.o `test -f 'variant_file_diff.cpp' || echo './'`variant_file_diff.cpp
mv -f .deps/vcftools-variant_file_diff.Tpo .deps/vcftools-variant_file_diff.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-variant_file_filters.o -MD -MP -MF .deps/vcftools-variant_file_filters.Tpo -c -o vcftools-variant_file_filters.o `test -f 'variant_file_filters.cpp' || echo './'`variant_file_filters.cpp
mv -f .deps/vcftools-variant_file_filters.Tpo .deps/vcftools-variant_file_filters.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-variant_file_format_convert.o -MD -MP -MF .deps/vcftools-variant_file_format_convert.Tpo -c -o vcftools-variant_file_format_convert.o `test -f 'variant_file_format_convert.cpp' || echo './'`variant_file_format_convert.cpp
mv -f .deps/vcftools-variant_file_format_convert.Tpo .deps/vcftools-variant_file_format_convert.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-variant_file_output.o -MD -MP -MF .deps/vcftools-variant_file_output.Tpo -c -o vcftools-variant_file_output.o `test -f 'variant_file_output.cpp' || echo './'`variant_file_output.cpp
mv -f .deps/vcftools-variant_file_output.Tpo .deps/vcftools-variant_file_output.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-vcf_entry.o -MD -MP -MF .deps/vcftools-vcf_entry.Tpo -c -o vcftools-vcf_entry.o `test -f 'vcf_entry.cpp' || echo './'`vcf_entry.cpp
mv -f .deps/vcftools-vcf_entry.Tpo .deps/vcftools-vcf_entry.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-vcf_entry_setters.o -MD -MP -MF .deps/vcftools-vcf_entry_setters.Tpo -c -o vcftools-vcf_entry_setters.o `test -f 'vcf_entry_setters.cpp' || echo './'`vcf_entry_setters.cpp
mv -f .deps/vcftools-vcf_entry_setters.Tpo .deps/vcftools-vcf_entry_setters.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-vcf_file.o -MD -MP -MF .deps/vcftools-vcf_file.Tpo -c -o vcftools-vcf_file.o `test -f 'vcf_file.cpp' || echo './'`vcf_file.cpp
mv -f .deps/vcftools-vcf_file.Tpo .deps/vcftools-vcf_file.Po
g++ -DHAVE_CONFIG_H -I. -I../..     -g -O2 -MT vcftools-vcftools.o -MD -MP -MF .deps/vcftools-vcftools.Tpo -c -o vcftools-vcftools.o `test -f 'vcftools.cpp' || echo './'`vcftools.cpp
mv -f .deps/vcftools-vcftools.Tpo .deps/vcftools-vcftools.Po
g++  -g -O2   -o vcftools vcftools-bcf_entry.o vcftools-bcf_entry_setters.o vcftools-bcf_file.o vcftools-bgzf.o vcftools-dgeev.o vcftools-entry.o vcftools-entry_filters.o vcftools-entry_getters.o vcftools-entry_setters.o vcftools-gamma.o vcftools-header.o vcftools-knetfile.o vcftools-output_log.o vcftools-parameters.o vcftools-variant_file.o vcftools-variant_file_diff.o vcftools-variant_file_filters.o vcftools-variant_file_format_convert.o vcftools-variant_file_output.o vcftools-vcf_entry.o vcftools-vcf_entry_setters.o vcftools-vcf_file.o vcftools-vcftools.o -lz   
make[3]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/cpp'
Making all in perl
make[3]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/perl'
make[3]: Nothing to be done for `all'.
make[3]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/perl'
make[3]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src'
make[3]: Nothing to be done for `all-am'.
make[3]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src'
make[2]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src'
make[2]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14'
make[2]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14'
make[1]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14'
cmccabe@DTV-A5211QLM:~/Desktop/NGS/vcftools-0.1.14$ sudo make install
[sudo] password for cmccabe: 
Making install in src
make[1]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src'
Making install in cpp
make[2]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/cpp'
make[3]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/cpp'
 /bin/mkdir -p '/usr/local/bin'
  /usr/bin/install -c vcftools '/usr/local/bin'
 /bin/mkdir -p '/usr/local/share/man/man1'
 /usr/bin/install -c -m 644 vcftools.1 '/usr/local/share/man/man1'
make[3]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/cpp'
make[2]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/cpp'
Making install in perl
make[2]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/perl'
make[3]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/perl'
 /bin/mkdir -p '/usr/local/bin'
 /usr/bin/install -c fill-aa fill-an-ac fill-fs fill-ref-md5 vcf-annotate vcf-compare vcf-concat vcf-consensus vcf-contrast vcf-convert vcf-fix-newlines vcf-fix-ploidy vcf-indel-stats vcf-isec vcf-merge vcf-phased-join vcf-query vcf-shuffle-cols vcf-sort vcf-stats vcf-subset vcf-to-tab vcf-tstv vcf-validator '/usr/local/bin'
 /bin/mkdir -p '/usr/local/share/perl/5.18.2'
 /usr/bin/install -c -m 644 FaSlice.pm Vcf.pm VcfStats.pm '/usr/local/share/perl/5.18.2'
make[3]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/perl'
make[2]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src/perl'
make[2]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src'
make[3]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src'
make[3]: Nothing to be done for `install-exec-am'.
make[3]: Nothing to be done for `install-data-am'.
make[3]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src'
make[2]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src'
make[1]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14/src'
make[1]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14'
make[2]: Entering directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14'
make[2]: Nothing to be done for `install-exec-am'.
make[2]: Nothing to be done for `install-data-am'.
make[2]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14'
make[1]: Leaving directory `/home/cmccabe/Desktop/NGS/vcftools-0.1.14'
    Tags: None
  • #2
    I think the executable is is /usr/local/bin.
    Since that folder is already in your PATH, you have nothing else to do.

    Comment

    • #3
      Yes, you are correct I do see the files at /usr/local/bin. However, I get the below error.

      Code:
      cmccabe@DTV-A5211QLM:~/Desktop/NGS$ cat /home/cmccabe/Desktop/vcf/getrm_NA12878_IDT_targets.vcf | vcftools_0.1.14/bin/vcf-annotate --fill-type | grep -oP "TYPE=\w+" | sort | uniq -c > output.bed
bash: vcftools_0.1.14/bin/vcf-annotate: No such file or directory

      Code:
      cmccabe@DTV-A5211QLM:~/Desktop/NGS$ echo $PATH
/home/cmccabe/Desktop/NGS/bedops-2.14.4/bin:/home/cmccabe/Desktop/NGS/samtools-1.2:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/home/cmccabe/Desktop/NGS/bedtools2-25.0/bin:/home/cmccabe/Desktop/NGS/bbmap-35.59:/home/cmccabe/Desktop/NGS/FastQC-0.11.4:/home/cmccabe/Desktop/NGS/bwa-0.7.12:/home/dnascopev/Desktop/picard-tools-1.140:/home/cmccabe/Desktop/NGS/fsfetch
      Do I need to move the individual files from /usr/local/bin to a bin folder within vcftools and add that to path? Thank you .

      Comment

      • #4
        If the executable file vcf-annotate is in /usr/local/bin, you can just call it directly.
        You don't need to specify any path.
        In this case, you are actually specifying the wrong path.

        If vcf-annotate is in /usr/local/bin, just type vcd-annotate to use it.
        If it isn't, jus type the full path, from the root, to use ist.

        Comment

        • #5
          Thank you very much. That seemed to solve it . This is a new way of installing that I am not used to but seems very nice. Thanks again.

          Comment

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