diff options
Diffstat (limited to 'gn/packages/bioinformatics.scm')
| -rw-r--r-- | gn/packages/bioinformatics.scm | 80 |
1 files changed, 24 insertions, 56 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm index 6a38499..45e88c7 100644 --- a/gn/packages/bioinformatics.scm +++ b/gn/packages/bioinformatics.scm @@ -428,45 +428,33 @@ reads.") (substitute-keyword-arguments (package-arguments edirect) ((#:phases phases) `(modify-phases ,phases - ; (replace 'build - ; (lambda* (#:key inputs #:allow-other-keys) - ; (let ((go (string-append (assoc-ref inputs "go") "/bin/go"))) - ; (invoke go "build" "xtract.go")))) - (add-after 'unpack 'unpack-binaries - (lambda* (#:key inputs #:allow-other-keys) - (let ((gzip (assoc-ref inputs "gzip")) - (xtract (assoc-ref inputs "xtract.Linux")) - (rchive (assoc-ref inputs "rchive.Linux"))) - (copy-file xtract "xtract.Linux.gz") - (copy-file rchive "rchive.Linux.gz") - (invoke (string-append gzip "/bin/gzip") "xtract.Linux.gz" "-dfv") - (invoke (string-append gzip "/bin/gzip") "rchive.Linux.gz" "-dfv")))) (add-after 'unpack 'patch-programs - (lambda _ - (substitute* (find-files "." "^e") - (("exec perl") "exec")) - (substitute* '("xtract" "rchive") - ;; or add current directory to PATH - ((".*PATH.*") "")) + (lambda* (#:key inputs #:allow-other-keys) + ;; Ignore errors about missing xtract.Linux and rchive.Linux. + (substitute* "pm-refresh" + (("cat \\\"\\$target") + "grep ^[[:digit:]] \"$target")) #t)) (replace 'install - (lambda* (#:key outputs #:allow-other-keys) - (let ((bin (string-append (assoc-ref outputs "out") "/bin"))) + (lambda* (#:key inputs outputs #:allow-other-keys) + (let ((bin (string-append (assoc-ref outputs "out") "/bin")) + (edirect-go (assoc-ref inputs "edirect-go-programs"))) (for-each (lambda (file) (install-file file bin)) - '("archive-pubmed" "asp-cp" "asp-ls" "download-pubmed" - "edirect.pl" "efetch" "epost" "esearch" "fetch-pubmed" - "ftp-cp" "ftp-ls" "has-asp" "pm-prepare" "pm-refresh" - "pm-stash" "rchive" "xtract")) - (install-file "xtract.Linux" bin) - (install-file "rchive.Linux" bin) - (chmod (string-append bin "/xtract.Linux") #o555) - (chmod (string-append bin "/rchive.Linux") #o555)) + '("archive-pubmed" "asp-cp" "asp-ls" "download-ncbi-data" + "download-pubmed" "edirect.pl" "efetch" "epost" "esearch" + "fetch-pubmed" "ftp-cp" "ftp-ls" "has-asp" "index-pubmed" + "pm-prepare" "pm-refresh" "pm-stash" "pm-collect" + "pm-index" "pm-invert" "pm-merge" "pm-promote")) + (symlink (string-append edirect-go "/bin/xtract.Linux") + (string-append bin "/xtract")) + (symlink (string-append edirect-go "/bin/rchive.Linux") + (string-append bin "/rchive"))) #t)) (replace 'wrap-program (lambda* (#:key outputs #:allow-other-keys) - ;; Make sure 'edirect.pl' finds all perl inputs at runtime. + ;; Make sure everything can run in a pure environment. (let ((out (assoc-ref outputs "out")) (path (getenv "PERL5LIB"))) (for-each @@ -474,44 +462,24 @@ reads.") (wrap-program file `("PERL5LIB" ":" prefix (,path))) (wrap-program file - `("PATH" ":" prefix (,(dirname (which "sed")) + `("PATH" ":" prefix (,(string-append out "/bin") + ,(dirname (which "sed")) ,(dirname (which "gzip")) + ,(dirname (which "grep")) + ,(dirname (which "perl")) ,(dirname (which "uname")))))) (find-files out "."))) #t)))))) (inputs - `(("gzip" ,gzip) + `(("edirect-go-programs" ,edirect-go-programs) ,@(package-inputs edirect))) - (native-inputs - `( - ;("go" ,go) - ("xtract.Linux" - ,(origin - (method url-fetch) - (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect" - "/versions/" (package-version edirect) - "/xtract.Linux.gz")) - (sha256 - (base32 - "1idzynn446qqjx2wv4jjgsx6cp349d4jy8g9z4gsg9l6sn5dhx53")))) - ("rchive.Linux" - ,(origin - (method url-fetch) - (uri (string-append "ftp://ftp.ncbi.nlm.nih.gov/entrez/entrezdirect/" - "/versions/" (package-version edirect) - "/rchive.Linux.gz")) - (sha256 - (base32 - "1p65hifv5d6nxg01vjwgy2nw49nssd822a8aj8jv412mhzj95ihv")))))) (native-search-paths ;; Ideally this should be set for LWP somewhere. (list (search-path-specification (variable "PERL_LWP_SSL_CA_FILE") (file-type 'regular) (separator #f) - (files '("/etc/ssl/certs/ca-certificates.crt"))))) - ;; Due to the precompiled binaries we download: - (supported-systems '("x86_64-linux")))) + (files '("/etc/ssl/certs/ca-certificates.crt"))))))) (define-public edirect-go-programs (package |