#!/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/y7hbjfvr5ry5cwhh1qpcf28vd8i29k9y-profile" (quote ("/gnu/store/lyz0xyrahphz49b95i19m6i4745wlpf7-guix-1.2.0-10.2386201" "/gnu/store/fvhj74pghapbjvsvj27skvkra1by1965-bash-minimal-5.0.16" "/gnu/store/ky1ndl1gj0pqk0alhvmps2xdrf347aqh-samtools-1.11" "/gnu/store/n8awazyldv9hbzb7pjcw76hiifmvrpvd-coreutils-8.32")))) "" (setenv "_GWL_PROFILE" "/gnu/store/y7hbjfvr5ry5cwhh1qpcf28vd8i29k9y-profile") (begin (for-each (lambda (pair) (setenv (car pair) (cdr pair))) (quote (("_GWL_PROCESS_NAME" . "sort_bam") ("_GWL_PROCESS_SYNOPSIS" . "") ("_GWL_PROCESS_DESCRIPTION" . "") ("_GWL_PROCESS_INPUTS" . "./output/mapped_reads/HBR_Rep1_Aligned.out.bam") ("_GWL_PROCESS_OUTPUT_PATH" . "") ("_GWL_PROCESS_OUTPUTS" . "./output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam ./output/logs/samtools_sort_HBR_Rep1.log") ("_GWL_PROCESS_COMPLEXITY_THREADS" . "") ("_GWL_PROCESS_COMPLEXITY_SPACE" . "") ("_GWL_PROCESS_COMPLEXITY_TIME" . "")))) (let ((retval (system* "/bin/sh" "-c" "\n mkdir -p ./output/logs\n samtools sort -o ./output/mapped_reads/HBR_Rep1_Aligned.sortedByCoord.out.bam ./output/mapped_reads/HBR_Rep1_Aligned.out.bam >> ./output/logs/samtools_sort_HBR_Rep1.log 2>&1\n "))) (or (zero? retval) (exit retval)))))