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gnu: homer: Install config.txt.

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* 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
This commit is contained in:
Ricardo Wurmus 2024-12-02 13:39:42 +01:00
parent af774e2780
commit d97a67d41d
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GPG key ID: 197A5888235FACAC
1 changed files with 17 additions and 3 deletions
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gnu/packages/bioinformatics.scm
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@ -7939,9 +7939,11 @@ indexing scheme is called a @dfn{Hierarchical Graph FM index} (HGFM).")
#:phases #:phases
#~(modify-phases %standard-phases #~(modify-phases %standard-phases
(replace 'configure (replace 'configure
(lambda _ (lambda* (#:key inputs #:allow-other-keys)
(let ((share (string-append #$output "/share/homer"))) (let ((share (string-append #$output "/share/homer")))
(mkdir-p share) (mkdir-p share)
(copy-file (assoc-ref inputs "config.txt")
(string-append share "/config.txt"))
(substitute* "configureHomer.pl" (substitute* "configureHomer.pl"
(("my \\$homeDir = \\$1;") (("my \\$homeDir = \\$1;")
(string-append "my $homeDir = \"" share "\";")))))) (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")) (string-append #$output "/bin/homer"))
(for-each patch-shebang (for-each patch-shebang
(find-files (string-append #$output "/share/homer/bin") (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 (inputs
(list perl)) (list perl))
(native-inputs (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") (home-page "http://homer.ucsd.edu/homer")
(synopsis "Motif discovery and next generation sequencing analysis") (synopsis "Motif discovery and next generation sequencing analysis")
(description (description