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  • cannot copy samtools-0.1.19/samtools to PATH

    I am installing Samtools and I got this message:

    Code:
    $ tar jxvf samtools-0.1.19.tar.bz2
    $ cd samtools-0.1.19
    $ make
    $ cd
    $ cp samtools-0.1.19/samtools $HOME/bin
    cp: cannot stat `samtools-0.1.19/samtools': No such file or directory
    I checked in the /samtools-0.1.19/ directory but there are nothing like "samtools" file but "samtools.1".

    I am using msys on window, would you mind giving me some advices?

    Thank you so much

  • #2
    Do NOT use samtools-0.0.19 at this time. It is ancient (in NGS age) and deprecated.

    Unless you must use it for some old software. Even then keep/use the latest version.

    Comment


    • #3
      Originally posted by GenoMax View Post
      Do NOT use samtools-0.0.19 at this time. It is ancient (in NGS age) and deprecated.

      Unless you must use it for some old software. Even then keep/use the latest version.
      I already tried with the latest version of "samtools" which is "samtools-1.4.1" but I still got that message

      Comment


      • #4
        Are you getting an error when compiling samtools?

        Comment


        • #5
          Originally posted by GenoMax View Post
          Are you getting an error when compiling samtools?
          Do you mean that do I got any error when running make command for samtools?

          Comment


          • #6
            That is correct.

            Comment


            • #7
              Originally posted by GenoMax View Post
              That is correct.
              I think I got this error :
              Code:
              bam_split.c:34:19: fatal error: regex.h: No such file or directory
               #include <regex.h>
                                 ^
              compilation terminated.
              make: *** [bam_split.o] Error 1
              here whole compiling process :
              Code:
              $ make
              Makefile:103: config.mk: No such file or directory
              config.mk:34: htslib-1.4.1/htslib_static.mk: No such file or directory
              cd htslib-1.4.1 && make htslib.pc.tmp
              make[1]: Entering directory `/c/RNA-seq-packages/samtools-1.4.1/htslib-1.4.1'
              sed -e '/^static_libs=/s/@static_LIBS@/-lz -lm -lbz2 -llzma/;s#@[^-][^@]*@##g' htslib.pc.in > htslib.pc.tmp
              make[1]: Leaving directory `/c/RNA-seq-packages/samtools-1.4.1/htslib-1.4.1'
              cd htslib-1.4.1 && make htslib_static.mk
              make[1]: Entering directory `/c/RNA-seq-packages/samtools-1.4.1/htslib-1.4.1'
              sed -n '/^static_libs=/s/[^=]*=/HTSLIB_static_LIBS = /p;/^static_ldflags=/s/[^=]*=/HTSLIB_static_LDFLAGS = /p' htslib.pc.tmp > htslib_static.mk
              make[1]: Leaving directory `/c/RNA-seq-packages/samtools-1.4.1/htslib-1.4.1'
              echo '/* Basic config.h generated by Makefile */' > config.h
              echo '#define HAVE_CURSES' >> config.h
              echo '#define HAVE_CURSES_H' >> config.h
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_index.o bam_index.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_plcmd.o bam_plcmd.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o sam_view.o sam_view.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_cat.o bam_cat.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_md.o bam_md.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_reheader.o bam_reheader.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_sort.o bam_sort.c
              bam_sort.c: In function 'ks_shuffle_heap':
              bam_sort.c:130:1: warning: implicit declaration of function 'drand48' [-Wimplicit-function-declaration]
               KSORT_INIT(heap, heap1_t, heap_lt)
               ^
              bam_sort.c: In function 'gen_unique_id':
              bam_sort.c:341:9: warning: implicit declaration of function 'lrand48' [-Wimplicit-function-declaration]
                       ksprintf(dest, "%s-%0lX", prefix, lrand48());
                       ^
              bam_sort.c:341:9: warning: format '%lX' expects argument of type 'long unsigned int', but argument 4 has type 'int' [-Wformat=]
              bam_sort.c: In function 'bam_merge':
              bam_sort.c:1529:5: warning: implicit declaration of function 'srand48' [-Wimplicit-function-declaration]
                   srand48(random_seed);
                   ^
              bam_sort.c: In function 'complain_about_memory_setting':
              bam_sort.c:1898:13: warning: unknown conversion type character 'z' in format [-Wformat=]
                           max_mem, suffix, SORT_MIN_MEGS_PER_THREAD);
                           ^
              bam_sort.c:1898:13: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'size_t' [-Wformat=]
              bam_sort.c:1898:13: warning: unknown conversion type character 'z' in format [-Wformat=]
              bam_sort.c:1898:13: warning: too many arguments for format [-Wformat-extra-args]
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bedidx.o bedidx.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_rmdup.o bam_rmdup.c
              bam_rmdup.c: In function 'bam_rmdup_core':
              bam_rmdup.c:157:21: warning: unknown conversion type character 'l' in format [-Wformat=]
                                   fprintf(stderr, "[bam_rmdup_core] %llu unmatched pairs\n", (long long)kh_size(del_set));
                                   ^
              bam_rmdup.c:157:21: warning: too many arguments for format [-Wformat-extra-args]
              bam_rmdup.c:216:21: warning: unknown conversion type character 'l' in format [-Wformat=]
                                   (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
                                   ^
              bam_rmdup.c:216:21: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_rmdup.c:216:21: warning: format '%lf' expects argument of type 'double', but argument 3 has type 'long long int' [-Wformat=]
              bam_rmdup.c:216:21: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long int' [-Wformat=]
              bam_rmdup.c:216:21: warning: too many arguments for format [-Wformat-extra-args]
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_rmdupse.o bam_rmdupse.c
              bam_rmdupse.c: In function 'bam_rmdupse_core':
              bam_rmdupse.c:199:21: warning: unknown conversion type character 'l' in format [-Wformat=]
                                   (long long)q->n_checked, (double)q->n_removed/q->n_checked, kh_key(aux, k));
                                   ^
              bam_rmdupse.c:199:21: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_rmdupse.c:199:21: warning: format '%lf' expects argument of type 'double', but argument 3 has type 'long long int' [-Wformat=]
              bam_rmdupse.c:199:21: warning: format '%s' expects argument of type 'char *', but argument 4 has type 'long long int' [-Wformat=]
              bam_rmdupse.c:199:21: warning: too many arguments for format [-Wformat-extra-args]
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_mate.o bam_mate.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_stat.o bam_stat.c
              bam_stat.c: In function 'bam_flagstat':
              bam_stat.c:159:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld in total (QC-passed reads + QC-failed reads)\n", s->n_reads[0], s->n_reads[1]);
                   ^
              bam_stat.c:159:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:159:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:160:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld secondary\n", s->n_secondary[0], s->n_secondary[1]);
                   ^
              bam_stat.c:160:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:160:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:161:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld supplementary\n", s->n_supp[0], s->n_supp[1]);
                   ^
              bam_stat.c:161:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:161:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:162:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld duplicates\n", s->n_dup[0], s->n_dup[1]);
                   ^
              bam_stat.c:162:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:162:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:163:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld mapped (%s : %s)\n", s->n_mapped[0], s->n_mapped[1], percent(b0, s->n_mapped[0], s->n_reads[0]), percent(b1, s->n_mapped[1], s->n_reads[1]));
                   ^
              bam_stat.c:163:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:163:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
              bam_stat.c:163:5: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
              bam_stat.c:163:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:164:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld paired in sequencing\n", s->n_pair_all[0], s->n_pair_all[1]);
                   ^
              bam_stat.c:164:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:164:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:165:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld read1\n", s->n_read1[0], s->n_read1[1]);
                   ^
              bam_stat.c:165:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:165:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:166:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld read2\n", s->n_read2[0], s->n_read2[1]);
                   ^
              bam_stat.c:166:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:166:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:167:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld properly paired (%s : %s)\n", s->n_pair_good[0], s->n_pair_good[1], percent(b0, s->n_pair_good[0], s->n_pair_all[0]), percent(b1, s->n_pair_good[1], s->n_pair_all[1]));
                   ^
              bam_stat.c:167:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:167:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
              bam_stat.c:167:5: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
              bam_stat.c:167:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:168:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld with itself and mate mapped\n", s->n_pair_map[0], s->n_pair_map[1]);
                   ^
              bam_stat.c:168:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:168:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:169:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld singletons (%s : %s)\n", s->n_sgltn[0], s->n_sgltn[1], percent(b0, s->n_sgltn[0], s->n_pair_all[0]), percent(b1, s->n_sgltn[1], s->n_pair_all[1]));
                   ^
              bam_stat.c:169:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:169:5: warning: format '%s' expects argument of type 'char *', but argument 2 has type 'long long int' [-Wformat=]
              bam_stat.c:169:5: warning: format '%s' expects argument of type 'char *', but argument 3 has type 'long long int' [-Wformat=]
              bam_stat.c:169:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:170:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld with mate mapped to a different chr\n", s->n_diffchr[0], s->n_diffchr[1]);
                   ^
              bam_stat.c:170:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:170:5: warning: too many arguments for format [-Wformat-extra-args]
              bam_stat.c:171:5: warning: unknown conversion type character 'l' in format [-Wformat=]
                   printf("%lld + %lld with mate mapped to a different chr (mapQ>=5)\n", s->n_diffhigh[0], s->n_diffhigh[1]);
                   ^
              bam_stat.c:171:5: warning: unknown conversion type character 'l' in format [-Wformat=]
              bam_stat.c:171:5: warning: too many arguments for format [-Wformat-extra-args]
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_color.o bam_color.c
              echo '#define SAMTOOLS_VERSION "1.4.1"' > version.h
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bamtk.o bamtk.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam2bcf.o bam2bcf.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam2bcf_indel.o bam2bcf_indel.c
              bam2bcf_indel.c: In function 'ks_shuffle_uint32_t':
              bam2bcf_indel.c:38:1: warning: implicit declaration of function 'drand48' [-Wimplicit-function-declaration]
               KSORT_INIT_GENERIC(uint32_t)
               ^
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o sample.o sample.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o cut_target.o cut_target.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o phase.o phase.c
              phase.c: In function 'ks_shuffle_rseq':
              phase.c:84:1: warning: implicit declaration of function 'drand48' [-Wimplicit-function-declaration]
               KSORT_INIT(rseq, frag_p, rseq_lt)
               ^
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam2depth.o bam2depth.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o padding.o padding.c
              padding.c: In function 'bam_pad2unpad':
              padding.c:218:17: warning: unknown conversion type character 'l' in format [-Wformat=]
                               fprintf(stderr, "[depad] ERROR: (Padded) length of '%s' is %u in BAM header, but %llu in embedded reference\n", bam_get_qname(b), h->target_len[r_tid], (unsigned long long)(r.l));
                               ^
              padding.c:218:17: warning: too many arguments for format [-Wformat-extra-args]
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bedcov.o bedcov.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bamshuf.o bamshuf.c
              bamshuf.c: In function 'ks_shuffle_bamshuf':
              bamshuf.c:78:1: warning: implicit declaration of function 'drand48' [-Wimplicit-function-declaration]
               KSORT_INIT(bamshuf, elem_t, elem_lt)
               ^
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o faidx.o faidx.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o dict.o dict.c
              dict.c: In function 'write_dict':
              dict.c:85:13: warning: implicit declaration of function 'realpath' [-Wimplicit-function-declaration]
                           char *real_path = realpath(fn, NULL);
                           ^
              dict.c:85:31: warning: initialization makes pointer from integer without a cast
                           char *real_path = realpath(fn, NULL);
                                             ^
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o stats.o stats.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o stats_isize.o stats_isize.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_flags.o bam_flags.c
              gcc -g -Wall -O2 -I. -Ihtslib-1.4.1  -c -o bam_split.o bam_split.c
              bam_split.c:34:19: fatal error: regex.h: No such file or directory
               #include <regex.h>
                                 ^
              compilation terminated.
              make: *** [bam_split.o] Error 1

              Comment


              • #8
                Originally posted by GenoMax View Post
                That is correct.
                I think I got this error :
                Code:
                bam_split.c:34:19: fatal error: regex.h: No such file or directory
                 #include <regex.h>
                                   ^
                compilation terminated.
                make: *** [bam_split.o] Error 1
                Attached file is the whole compiling process.
                Attached Files

                Comment


                • #9
                  Since you are getting an error the program has not actually compiled.

                  Are you using linux shell on Windows 10 or a cygwin/VM environment?

                  Comment


                  • #10
                    Originally posted by GenoMax View Post
                    Since you are getting an error the program has not actually compiled.

                    Are you using linux shell on Windows 10 or a cygwin/VM environment?
                    I am using minGW/msys on win10

                    Comment


                    • #11
                      Install the regex.h for MinGW from here (probably in /usr/include).

                      Comment


                      • #12
                        Originally posted by GenoMax View Post
                        Install the regex.h for MinGW from here (probably in /usr/include).
                        I have just installed linux and I could install samtools without any problem anymore, thank you so much for your help.

                        Comment

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