diff options
Diffstat (limited to 'scripts')
| -rwxr-xr-x | scripts/create-singularity-pangenome-tools.sh | 32 |
1 files changed, 20 insertions, 12 deletions
diff --git a/scripts/create-singularity-pangenome-tools.sh b/scripts/create-singularity-pangenome-tools.sh index f25fbbf..837f720 100755 --- a/scripts/create-singularity-pangenome-tools.sh +++ b/scripts/create-singularity-pangenome-tools.sh @@ -73,30 +73,38 @@ INVENTORY="$DEST_DIR/pangenome-tools-guix-bioinformatics-$GB_HASH-$DATE-$HASH.md TOOLS_TSV=$(mktemp) trap 'rm -f "$TOOLS_TSV"' EXIT guix repl -L "$CHANNEL_DIR" -- /dev/stdin > "$TOOLS_TSV" <<'SCM' -(use-modules (guix packages) (gn packages pangenome) (ice-9 format)) +(use-modules (guix packages) (guix utils) (gn packages pangenome) + (ice-9 format) (ice-9 regex)) +;; Only keep packages defined in gn/packages/pangenome.scm or +;; gn/packages/pangenome-rust.scm -- those are the real pangenome +;; tools; everything else (libc, R, python, coreutils, ...) is +;; infrastructure that ends up in the closure but isn't user-facing. +(define pangenome-file-rx + (make-regexp "gn/packages/pangenome(-rust)?\\.scm$")) +(define (pangenome-package? p) + (let ((loc (package-location p))) + (and loc + (regexp-exec pangenome-file-rx (location-file loc))))) (define seen (make-hash-table)) +(define meta-packages + '("pangenomes" "mempang-workshop-pangenomes" "mempang-workshop")) (define (emit p) - (unless (hash-ref seen (package-name p)) + (when (and (pangenome-package? p) + (not (member (package-name p) meta-packages)) + (not (hash-ref seen (package-name p)))) (hash-set! seen (package-name p) #t) (format #t "~a\t~a\t~a~%" (package-name p) (package-version p) (or (package-synopsis p) "")))) (define (expand x) (let ((p (if (pair? x) (cadr x) x))) - (cond - ((member (package-name p) - '("mempang-workshop-pangenomes" "pangenomes")) - (for-each expand (package-propagated-inputs p))) - (else (emit p))))) + (emit p) + (for-each expand (package-propagated-inputs p)))) (for-each expand (package-propagated-inputs mempang-workshop)) SCM CLEAN_TSV=$(mktemp) trap 'rm -f "$TOOLS_TSV" "$CLEAN_TSV"' EXIT -# Strip generic Unix utilities, compilers, and the base R/Python -# ecosystems so the inventory only lists pangenome-relevant tools. -EXCLUDE='^(bc|coreutils|gawk|gcc|grep|gzip|parallel|pigz|sed|wget|which|zstd|python|python-.*|r-minimal|r-.*)\t' -grep -P '^[a-z0-9]' "$TOOLS_TSV" \ - | grep -vP "$EXCLUDE" > "$CLEAN_TSV" +grep -P '^[a-z0-9]' "$TOOLS_TSV" > "$CLEAN_TSV" # Compute column widths so the rendered Markdown table is also # readable as raw text. |