#!/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)))))