diff mbox

gnu: Add SEEK.

Message ID 20160615133140.13125-2-ricardo.wurmus@mdc-berlin.de
State New
Headers

Commit Message

Ricardo Wurmus June 15, 2016, 1:31 p.m. UTC 
  * gnu/packages/bioinformatics.scm (seek): New variable.
---
 gnu/packages/bioinformatics.scm | 74 +++++++++++++++++++++++++++++++++++++++++
 1 file changed, 74 insertions(+)

Comments

Alex Kost June 15, 2016, 7:50 p.m. UTC | #1 
Ricardo Wurmus (2016-06-15 16:31 +0300) wrote:

> * gnu/packages/bioinformatics.scm (seek): New variable.
> ---
>  gnu/packages/bioinformatics.scm | 74 +++++++++++++++++++++++++++++++++++++++++
>  1 file changed, 74 insertions(+)
[...]
> +(define-public seek
> +  ;; There are no release tarballs.  According to the installation
> +  ;; instructions at http://seek.princeton.edu/installation.jsp, the latest
> +  ;; stable release is identified by this changeset ID.
> +  (let ((changeset "2329130")
> +        (revision "1"))
> +    (package
> +      (name "seek")
> +      (version (string-append "0-" revision "." changeset))
> +      (source (origin
> +                (method hg-fetch)
> +                (uri (hg-reference
> +                      (url "https://bitbucket.org/libsleipnir/sleipnir")
> +                      (changeset changeset)))
> +                (sha256
> +                 (base32
> +                  "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
> +      (build-system gnu-build-system)
> +      (arguments
> +       `(#:modules ((srfi srfi-1)
> +                    (guix build gnu-build-system)
> +                    (guix build utils))
> +         #:phases
> +         (let ((dirs '("SeekMiner"
> +                       "SeekEvaluator"
> +                       "SeekPrep"
> +                       "Distancer"
> +                       "Data2DB"
> +                       "PCL2Bin")))
> +           (modify-phases %standard-phases
> +             (add-before 'configure 'bootstrap
> +               (lambda _
> +                 (zero? (system* "bash" "gen_auto"))))
> +             (add-after 'build 'build-additional-tools
> +               (lambda* (#:key make-flags #:allow-other-keys)
> +                 (fold (lambda (dir result)
> +                         (with-directory-excursion (string-append "tools/" dir)
> +                           (and result
> +                                (zero? (apply system*
> +                                              `("make" ,@make-flags))))))

or just: (zero? (apply system* "make" make-flags))

Is 'fold' really needed here?  What about:

  (every (lambda (dir)
           (with-directory-excursion (string-append "tools/" dir)
             (zero? (apply system* "make" make-flags))))
         dirs)

> +                       #t dirs)))
> +             (add-after 'install 'install-additional-tools
> +               (lambda* (#:key make-flags #:allow-other-keys)
> +                 (fold (lambda (dir result)
> +                         (with-directory-excursion (string-append "tools/" dir)
> +                           (and result
> +                                (zero? (apply system*
> +                                              `("make" ,@make-flags "install"))))))
> +                       #t dirs)))))))
> +      (inputs
> +       `(("gsl" ,gsl)
> +         ("boost" ,boost)
> +         ("libsvm" ,libsvm)
> +         ("readline" ,readline)
> +         ("gengetopt" ,gengetopt)
> +         ("log4cpp" ,log4cpp)))
> +      (native-inputs
> +       `(("autoconf" ,autoconf)
> +         ("automake" ,automake)
> +         ("perl" ,perl)))
> +      (home-page "http://seek.princeton.edu")
> +      (synopsis "Gene co-expression search engine")
> +      (description
> +       "SEEK is a computational gene co-expression search engine.  SEEK provides
> +biologists with a way to navigate the massive human expression compendium that
> +now contains thousands of expression datasets.  SEEK returns a robust ranking
> +of co-expressed genes in the biological area of interest defined by the user's
> +query genes.  It also prioritizes thousands of expression datasets according
> +to the user's query of interest.")
> +      (license license:cc-by3.0))))
> +
>  (define-public samtools
>    (package
>      (name "samtools")
Ricardo Wurmus June 28, 2016, 8:50 p.m. UTC | #2 
Alex Kost <alezost@gmail.com> writes:

> Ricardo Wurmus (2016-06-15 16:31 +0300) wrote:
>
>> * gnu/packages/bioinformatics.scm (seek): New variable.

[…]

> Is 'fold' really needed here?  What about:
>
>   (every (lambda (dir)
>            (with-directory-excursion (string-append "tools/" dir)
>              (zero? (apply system* "make" make-flags))))
>          dirs)

No, “fold” is not needed.  I always forget that we have “every”.  Thanks
for the reminder!  I changed it and pushed to master.

~~ Ricardo
diff mbox

Patch

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index d5f5500..71cf147 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -27,6 +27,7 @@ 
   #:use-module (guix utils)
   #:use-module (guix download)
   #:use-module (guix git-download)
+  #:use-module (guix hg-download)
   #:use-module (guix build-system ant)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
@@ -51,6 +52,7 @@ 
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages java)
   #:use-module (gnu packages linux)
+  #:use-module (gnu packages logging)
   #:use-module (gnu packages machine-learning)
   #:use-module (gnu packages maths)
   #:use-module (gnu packages mpi)
@@ -61,6 +63,7 @@ 
   #:use-module (gnu packages popt)
   #:use-module (gnu packages protobuf)
   #:use-module (gnu packages python)
+  #:use-module (gnu packages readline)
   #:use-module (gnu packages ruby)
   #:use-module (gnu packages statistics)
   #:use-module (gnu packages tbb)
@@ -3145,6 +3148,77 @@  while RNA-seq specific modules evaluate sequencing saturation, mapped reads
 distribution, coverage uniformity, strand specificity, etc.")
     (license license:gpl3+)))
 
+(define-public seek
+  ;; There are no release tarballs.  According to the installation
+  ;; instructions at http://seek.princeton.edu/installation.jsp, the latest
+  ;; stable release is identified by this changeset ID.
+  (let ((changeset "2329130")
+        (revision "1"))
+    (package
+      (name "seek")
+      (version (string-append "0-" revision "." changeset))
+      (source (origin
+                (method hg-fetch)
+                (uri (hg-reference
+                      (url "https://bitbucket.org/libsleipnir/sleipnir")
+                      (changeset changeset)))
+                (sha256
+                 (base32
+                  "0qrvilwh18dpbhkf92qvxbmay0j75ra3jg2wrhz67gf538zzphsx"))))
+      (build-system gnu-build-system)
+      (arguments
+       `(#:modules ((srfi srfi-1)
+                    (guix build gnu-build-system)
+                    (guix build utils))
+         #:phases
+         (let ((dirs '("SeekMiner"
+                       "SeekEvaluator"
+                       "SeekPrep"
+                       "Distancer"
+                       "Data2DB"
+                       "PCL2Bin")))
+           (modify-phases %standard-phases
+             (add-before 'configure 'bootstrap
+               (lambda _
+                 (zero? (system* "bash" "gen_auto"))))
+             (add-after 'build 'build-additional-tools
+               (lambda* (#:key make-flags #:allow-other-keys)
+                 (fold (lambda (dir result)
+                         (with-directory-excursion (string-append "tools/" dir)
+                           (and result
+                                (zero? (apply system*
+                                              `("make" ,@make-flags))))))
+                       #t dirs)))
+             (add-after 'install 'install-additional-tools
+               (lambda* (#:key make-flags #:allow-other-keys)
+                 (fold (lambda (dir result)
+                         (with-directory-excursion (string-append "tools/" dir)
+                           (and result
+                                (zero? (apply system*
+                                              `("make" ,@make-flags "install"))))))
+                       #t dirs)))))))
+      (inputs
+       `(("gsl" ,gsl)
+         ("boost" ,boost)
+         ("libsvm" ,libsvm)
+         ("readline" ,readline)
+         ("gengetopt" ,gengetopt)
+         ("log4cpp" ,log4cpp)))
+      (native-inputs
+       `(("autoconf" ,autoconf)
+         ("automake" ,automake)
+         ("perl" ,perl)))
+      (home-page "http://seek.princeton.edu")
+      (synopsis "Gene co-expression search engine")
+      (description
+       "SEEK is a computational gene co-expression search engine.  SEEK provides
+biologists with a way to navigate the massive human expression compendium that
+now contains thousands of expression datasets.  SEEK returns a robust ranking
+of co-expressed genes in the biological area of interest defined by the user's
+query genes.  It also prioritizes thousands of expression datasets according
+to the user's query of interest.")
+      (license license:cc-by3.0))))
+
 (define-public samtools
   (package
     (name "samtools")