diff options
| author | Ricardo Wurmus <rekado@elephly.net> | 2024-12-02 13:39:42 +0100 |
|---|---|---|
| committer | Ricardo Wurmus <rekado@elephly.net> | 2024-12-02 13:41:08 +0100 |
| commit | d97a67d41de142c0fbdba55e96bfc147482bfae2 (patch) | |
| tree | 98f81f8c6d710acf12270b771fc19d1084128f1a | |
| parent | af774e278057f3e1da210c2862c0450c3b988220 (diff) | |
gnu: homer: Install config.txt.
* gnu/packages/bioinformatics.scm (homer)[native-inputs]: Add config.txt.
[arguments]: Update 'configure phase to place config.txt in expected location;
patch configuration code to optionally load a user's configuration file.
Change-Id: Ib05c828e751c6568524bbef45997a42fade4545a
| -rw-r--r-- | gnu/packages/bioinformatics.scm | 20 |
1 files changed, 17 insertions, 3 deletions
diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index 3df45060470..c761344dedf 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -7939,9 +7939,11 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") #:phases #~(modify-phases %standard-phases (replace 'configure - (lambda _ + (lambda* (#:key inputs #:allow-other-keys) (let ((share (string-append #$output "/share/homer"))) (mkdir-p share) + (copy-file (assoc-ref inputs "config.txt") + (string-append share "/config.txt")) (substitute* "configureHomer.pl" (("my \\$homeDir = \\$1;") (string-append "my $homeDir = \"" share "\";")))))) @@ -7963,11 +7965,23 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).") (string-append #$output "/bin/homer")) (for-each patch-shebang (find-files (string-append #$output "/share/homer/bin") - "\\.pl$"))))))) + "\\.pl$")) + ;; Also load config file from user's home directory. + (substitute* (string-append #$output "/share/homer/bin/HomerConfig.pm") + (("#parseConfigFile") "parseConfigFile"))))))) (inputs (list perl)) (native-inputs - (list perl unzip)) + `(("perl" ,perl) + ("unzip" ,unzip) + ("config.txt" + ,(origin + (method url-fetch) + (uri (string-append "https://web.archive.org/web/20200531014112id_/" + "http://homer.ucsd.edu/homer/update.txt")) + (sha256 + (base32 + "1hf17pk8r6b297ysd27bvxzyn8pxdhxd8wj8g0lqlifbid9fw04h")))))) (home-page "http://homer.ucsd.edu/homer") (synopsis "Motif discovery and next generation sequencing analysis") (description |