#!/gnu/store/m5iprcg6pb5ch86r9agmqwd8v6kp7999-guile-3.0.5/bin/guile --no-auto-compile
!#
(begin
  (set! %load-path
        (cons
         (string-append "/gnu/store/lyz0xyrahphz49b95i19m6i4745wlpf7-guix-1.2.0-10.2386201" "/share/guile/site/"
                        (effective-version))
         %load-path))
  (set! %load-compiled-path
        (cons
         (string-append "/gnu/store/lyz0xyrahphz49b95i19m6i4745wlpf7-guix-1.2.0-10.2386201" "/lib/guile/"
                        (effective-version)
                        "/site-ccache")
         %load-compiled-path))
  (use-modules
   (guix search-paths))
  (set-search-paths
   (map sexp->search-path-specification
        (quote
         (("PATH"
           ("bin" "sbin")
           ":" directory #f)
          ("GUIX_EXTENSIONS_PATH"
           ("share/guix/extensions")
           ":" directory #f)
          ("BASH_LOADABLES_PATH"
           ("lib/bash")
           ":" directory #f))))
   (cons "/gnu/store/8fb0nkg1y32797rxybr1l944vny85fcf-profile"
         (quote
          ("/gnu/store/lyz0xyrahphz49b95i19m6i4745wlpf7-guix-1.2.0-10.2386201" "/gnu/store/fvhj74pghapbjvsvj27skvkra1by1965-bash-minimal-5.0.16" "/gnu/store/hzx0iyg1a637zywcbhv3l9lk9fkyihgs-sed-4.8" "/gnu/store/r2b6y68r5khf7y0lm0iyhms58yhi2z4p-htseq-0.9.1" "/gnu/store/n8awazyldv9hbzb7pjcw76hiifmvrpvd-coreutils-8.32"))))
  ""
  (setenv "_GWL_PROFILE" "/gnu/store/8fb0nkg1y32797rxybr1l944vny85fcf-profile")
  (begin
    (for-each
     (lambda
         (pair)
       (setenv
        (car pair)
        (cdr pair)))
     (quote
      (("_GWL_PROCESS_NAME" . "htseq_count")
       ("_GWL_PROCESS_SYNOPSIS" . "")
       ("_GWL_PROCESS_DESCRIPTION" . "")
       ("_GWL_PROCESS_INPUTS" . "sample_data/sample.gtf ./output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam ./output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam ./output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam ./output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam ./output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam ./output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam")
       ("_GWL_PROCESS_OUTPUT_PATH" . "")
       ("_GWL_PROCESS_OUTPUTS" . "./output/feature_counts/raw_counts/htseq_stats.txt ./output/feature_counts/raw_counts/counts_from_star_htseq-count.txt ./output/logs/htseq-count.log")
       ("_GWL_PROCESS_COMPLEXITY_THREADS" . "")
       ("_GWL_PROCESS_COMPLEXITY_SPACE" . "")
       ("_GWL_PROCESS_COMPLEXITY_TIME" . ""))))
    (let
        ((retval
          (system* "/bin/sh" "-c" "\n        echo HBR_Rep1 HBR_Rep2 HBR_Rep3 UHR_Rep1 UHR_Rep2 UHR_Rep3 | sed 's/ /\\t/g' > ./output/feature_counts/raw_counts/htseq_out.txt\n        htseq-count ./output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam ./output/mapped_reads/HBR_Rep2_Aligned.sortedByCoord.out.bam ./output/mapped_reads/HBR_Rep3_Aligned.sortedByCoord.out.bam ./output/mapped_reads/UHR_Rep1_Aligned.sortedByCoord.out.bam ./output/mapped_reads/UHR_Rep2_Aligned.sortedByCoord.out.bam ./output/mapped_reads/UHR_Rep3_Aligned.sortedByCoord.out.bam sample_data/sample.gtf 1>> ./output/feature_counts/raw_counts/htseq_out.txt 2>> ./output/logs/htseq-count.log\n\n        # move feature count stats (e.g. __no_feature etc) to another file\n        echo HBR_Rep1 HBR_Rep2 HBR_Rep3 UHR_Rep1 UHR_Rep2 UHR_Rep3 > ./output/feature_counts/raw_counts/htseq_stats.txt\n        tail -n 5 ./output/feature_counts/raw_counts/htseq_out.txt >> ./output/feature_counts/raw_counts/htseq_stats.txt\n\n        # only keep feature counts in the counts table (remove stats)\n        head -n -5 ./output/feature_counts/raw_counts/htseq_out.txt > ./output/feature_counts/raw_counts/counts_from_star_htseq-count.txt\n\n        # remove temp file\n        rm ./output/feature_counts/raw_counts/htseq_out.txt\n    ")))
      (or
       (zero? retval)
       (exit retval)))))

Generated by Ricardo Wurmus using scpaste at Fri Jan 22 12:05:39 2021. CET. (original)