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-rw-r--r--gn/packages/bioinformatics.scm388
-rw-r--r--gn/packages/genenetwork.scm57
-rw-r--r--gn/packages/python.scm6
3 files changed, 428 insertions, 23 deletions
diff --git a/gn/packages/bioinformatics.scm b/gn/packages/bioinformatics.scm
index b503e22..295a2b3 100644
--- a/gn/packages/bioinformatics.scm
+++ b/gn/packages/bioinformatics.scm
@@ -20,6 +20,7 @@
   #:use-module (gnu packages boost)
   #:use-module (gnu packages compression)
   #:use-module (gnu packages databases)
+  #:use-module (gnu packages cmake)
   #:use-module (gnu packages cpio)
   #:use-module (gnu packages file)
   #:use-module (gnu packages gcc)
@@ -48,6 +49,221 @@
   #:use-module (gn packages statistics)
   #:use-module (srfi srfi-1))
 
+(define-public freec
+  (package
+    (name "control-freec")
+    (version "8.7")
+    (source (origin
+      (method url-fetch)
+      (uri "http://bioinfo-out.curie.fr/projects/freec/src/FREEC_Linux64.tar.gz")
+      (file-name (string-append name "-" version ".tar.gz"))
+      (sha256
+       (base32 "12sl7gxbklhvv0687qjhml1z4lwpcn159zcyxvawvclsrzqjmv0h"))))
+    (build-system gnu-build-system)
+    ;; The source code's filename indicates only a 64-bit Linux build.
+    ;; We need to investigate whether this is true.
+    (supported-systems '("x86_64-linux"))
+    (arguments
+     `(#:phases
+       (modify-phases %standard-phases
+         ;; There's no configure phase because there are no external
+         ;; dependencies.
+         (delete 'configure)
+         ;; There are no tests.
+         (delete 'check)
+         (replace
+          'unpack
+          (lambda* (#:key source #:allow-other-keys)
+            (and
+             (zero? (system* "mkdir" "source"))
+             (with-directory-excursion "source"
+               (zero? (system* "tar" "xvf" source))))))
+         (replace
+          'build
+          (lambda* (#:key inputs #:allow-other-keys)
+            (with-directory-excursion "source"
+              (zero? (system* "make")))))
+         (replace
+          'install
+          (lambda* (#:key outputs #:allow-other-keys)
+            (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+              (install-file "source/freec" bin)))))))
+    (home-page "http://bioinfo-out.curie.fr/projects/freec/")
+    (synopsis "Tool for detection of copy-number changes and allelic imbalances
+(including LOH) using deep-sequencing data")
+    (description "Control-FREEC automatically computes, normalizes, segments
+copy number and beta allele frequency (BAF) profiles, then calls copy number
+alterations and LOH.  The control (matched normal) sample is optional for whole
+genome sequencing data but mandatory for whole exome or targeted sequencing
+data.  For whole genome sequencing data analysis, the program can also use
+mappability data (files created by GEM). ")
+    (license license:gpl2+)))
+
+(define-public freebayes
+  (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
+    (package
+      (name "freebayes")
+      (version (string-append "v1.0.2-" (string-take commit 7)))
+      (source (origin
+        (method git-fetch)
+        (uri (git-reference
+          (url "https://github.com/ekg/freebayes.git")
+          (commit commit)))
+        (file-name (string-append name "-" version "-checkout"))
+        (sha256
+         (base32 "1sbzwmcbn78ybymjnhwk7qc5r912azy5vqz2y7y81616yc3ba2a2"))))
+      (build-system gnu-build-system)
+      (native-inputs
+       `(("cmake" ,cmake)
+         ("htslib" ,htslib)
+         ("zlib" ,zlib)
+         ("python" ,python-2)
+         ("perl" ,perl)
+         ("bamtools-src"
+          ,(origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/ekg/bamtools/archive/"
+                  "e77a43f5097ea7eee432ee765049c6b246d49baa" ".tar.gz"))
+             (file-name "bamtools-src.tar.gz")
+             (sha256
+              (base32 "0rqymka21g6lfjfgxzr40pxz4c4fcl77jpy1np1li70pnc7h2cs1"))))
+         ("vcflib-src"
+          ,(origin
+             (method url-fetch)
+             (uri (string-append "https://github.com/vcflib/vcflib/archive/"
+                  "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz"))
+             (file-name "vcflib-5ac0913.tar.gz")
+             (sha256
+              (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8"))))
+         ;; These are submodules for the vcflib version used in freebayes
+         ("tabixpp-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/tabixpp/archive/"
+                  "bbc63a49acc52212199f92e9e3b8fba0a593e3f7" ".tar.gz"))
+            (file-name "tabixpp-src.tar.gz")
+            (sha256
+             (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77"))))
+         ("intervaltree-src"
+          ,(origin
+             (method url-fetch)
+             (uri (string-append
+                   "https://github.com/ekg/intervaltree/archive/"
+                   "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz"))
+             (file-name "intervaltree-src.tar.gz")
+             (sha256
+              (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))
+         ("smithwaterman-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/smithwaterman/archive/"
+                  "203218b47d45ac56ef234716f1bd4c741b289be1" ".tar.gz"))
+            (file-name "smithwaterman-src.tar.gz")
+            (sha256
+             (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b"))))
+         ("multichoose-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/multichoose/archive/"
+                  "73d35daa18bf35729b9ba758041a9247a72484a5" ".tar.gz"))
+            (file-name "multichoose-src.tar.gz")
+            (sha256
+             (base32 "07aizwdabmlnjaq4p3v0vsasgz1xzxid8xcxcw3paq8kh9c1099i"))))
+         ("fsom-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/fsom/archive/"
+                  "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz"))
+            (file-name "fsom-src.tar.gz")
+            (sha256
+             (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3"))))
+         ("filevercmp-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/filevercmp/archive/"
+                  "1a9b779b93d0b244040274794d402106907b71b7" ".tar.gz"))
+            (file-name "filevercmp-src.tar.gz")
+            (sha256
+             (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
+         ("fastahack-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/fastahack/archive/"
+                  "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd" ".tar.gz"))
+            (file-name "fastahack-src.tar.gz")
+            (sha256
+             (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2"))))
+            ))
+      (arguments
+       `(#:tests? #f
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (delete 'check)
+           (add-after 'unpack 'unpack-submodule-sources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((unpack (lambda (source target)
+                               (with-directory-excursion target
+                                 (zero? (system* "tar" "xvf"
+                                        (assoc-ref inputs source)
+                                        "--strip-components=1"))))))
+                 (and
+                  (unpack "bamtools-src" "bamtools")
+                  (unpack "vcflib-src" "vcflib")
+                  (unpack "intervaltree-src" "intervaltree")
+                  (unpack "fastahack-src" "vcflib/fastahack")
+                  (unpack "filevercmp-src" "vcflib/filevercmp")
+                  (unpack "fsom-src" "vcflib/fsom")
+                  (unpack "intervaltree-src" "vcflib/intervaltree")
+                  (unpack "multichoose-src" "vcflib/multichoose")
+                  (unpack "smithwaterman-src" "vcflib/smithwaterman")
+                  (unpack "tabixpp-src" "vcflib/tabixpp")))))
+           (add-after 'unpack-submodule-sources 'fix-makefile
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* '("vcflib/Makefile")
+                 (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0"))))
+           (replace
+            'build
+            (lambda* (#:key inputs make-flags #:allow-other-keys)
+              (and
+               ;; We must compile Bamtools before we can compile the main
+               ;; project.
+               (with-directory-excursion "bamtools"
+                 (system* "mkdir" "build")
+                 (with-directory-excursion "build"
+                   (and (zero? (system* "cmake" "../"))
+                        (zero? (system* "make")))))
+               ;; We must compile vcflib before we can compile the main
+               ;; project.
+               (with-directory-excursion "vcflib"
+                 (with-directory-excursion "tabixpp"
+                   (zero? (system* "make")))
+                 (zero? (system* "make" "CC=gcc"
+                   (string-append "CFLAGS=\"" "-Itabixpp "
+                     "-I" (assoc-ref inputs "htslib") "/include " "\"") "all")))
+
+               (with-directory-excursion "src"
+                 (zero? (system* "make"))))))
+           (replace
+            'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((bin (string-append (assoc-ref outputs "out") "/bin")))
+                (install-file "bin/freebayes" bin)
+                (install-file "bin/bamleftalign" bin))))
+           ;; (replace
+           ;;  'check
+           ;;  (lambda* (#:key outputs #:allow-other-keys)
+           ;;    (with-directory-excursion "test"
+           ;;      (zero? (system* "make" "test")))))
+             )))
+      (home-page "https://github.com/ekg/freebayes")
+      (synopsis "haplotype-based variant detector.")
+      (description "FreeBayes is a Bayesian genetic variant detector designed to
+find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms),
+indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and
+complex events (composite insertion and substitution events) smaller than the
+length of a short-read sequencing alignment.")
+      (license license:expat))))
 
 (define-public r-biocpreprocesscore
   (package
@@ -69,7 +285,6 @@
      "A library of core preprocessing routines.")
     (license license:lgpl2.0+)))
 
-
 (define-public r-wgcna
   (let ((commit "425bc170cc0873ddbd414675ac40f6d4d724c7cb"))
 (package
@@ -305,37 +520,48 @@ association studies (GWAS).")
     (license license:gpl3))))
 
 (define-public sambamba
-  (let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
+  (let ((commit "c810c7ef14957f16288c205fd7b9d25c4ae7005d"))
+  ;;(let ((commit "2ca5a2dbac5ab90c3b4c588519edc3edcb71df84"))
     (package
       (name "sambamba")
       (version (string-append "0.5.9-1." (string-take commit 7)))
       (source (origin
         (method git-fetch)
-        (uri (git-reference                
-              (url "https://github.com/pjotrp/sambamba.git")
+        (uri (git-reference
+              (url "https://github.com/roelj/sambamba.git")
+              ;;(url "https://github.com/pjotrp/sambamba.git")
               (commit commit)))
         (file-name (string-append name "-" version "-checkout"))
         (sha256
          (base32
-          "1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"))))
+          "0c4c13f021sl7mf5xc2v8dbwsz775n8dlsrrn7qa6qgbx05n54dv"))))
+          ;;"1f14wn9aaxwjkmla6pzq3s28741carbr2v0fd2v2mm1dcpwnrqz5"))))
       (build-system gnu-build-system)
       (native-inputs
        `(("ldc" ,ldc)
-         ("lz4" ,lz4)
+         ;;("lz4" ,lz4)
          ("rdmd" ,rdmd)
          ("zlib" ,zlib)
-         ("perl" ,perl) ; Needed for htslib tests?
-         ("ruby" ,ruby) ; Needed for htslib tests?
-         ("python" ,python) ; Needed for htslib tests?
+         ("perl" ,perl) ; Needed for htslib
+         ("ruby" ,ruby) ; Needed for htslib
+         ("python" ,python) ; Needed for htslib
          ("gcc" ,gcc)
+         ("lz4-src"
+          ,(origin
+             (method url-fetch)
+             (uri "https://github.com/Cyan4973/lz4/archive/160661c7a4cbf805f4af74d2e3932a17a66e6ce7.tar.gz")
+             (sha256
+              (base32 "131nnbsd5dh7c8sdqzc9kawh3mi0qi4qxznv7zhzfszlx4g2fd20"))))
          ("htslib-src"
           ,(origin
              (method url-fetch)
-             (uri "https://github.com/samtools/htslib/archive/1.3.tar.gz")
-             (file-name "htslib-1.3.tar.gz")
+             (uri "https://github.com/lomereiter/htslib/archive/2f3c3ea7b301f9b45737a793c0b2dcf0240e5ee5.tar.gz")
+             ;;(uri "https://github.com/samtools/htslib/archive/1.3.tar.gz")
+             ;;(file-name "htslib-1.3.tar.gz")
              (sha256
-              (base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9"))
-             (patches (list (search-patch "htslib-add-cram_to_bam.patch")))))
+              (base32 "0bl6w856afnbgdsw8bybsxpqsyf2ba3f12rqh47hhpxvv866g08w"))))
+              ;;(base32 "1bqkif7yrqmiqak5yb74kgpb2lsdlg7y344qa1xkdg7k1l4m86i9"))
+             ;;(patches (list (search-patch "htslib-add-cram_to_bam.patch")))))
          ("biod-src"
           ,(origin
              (method git-fetch)
@@ -360,14 +586,17 @@ association studies (GWAS).")
                (and (with-directory-excursion "htslib"
                       (zero? (system* "tar" "xvf" (assoc-ref inputs "htslib-src")
                                       "--strip-components=1")))
+                    (with-directory-excursion "lz4"
+                      (zero? (system* "tar" "xvf" (assoc-ref inputs "lz4-src")
+                                      "--strip-components=1")))
                     (zero? (system* "rm" "-r" "BioD"))
                     (zero? (system* "ln" "--symbolic" "--no-target-directory"
                                     (assoc-ref inputs "biod-src") "BioD")))))
            (replace
             'build
             (lambda* (#:key inputs make-flags #:allow-other-keys)
-              (zero? (system* "make" "-f" "Makefile.guix"
-                              (string-append "LDC_LIB_PATH="
+              (zero? (system* "make" "sambamba-ldmd2-64" "CC=gcc" "D_COMPILER=ldc2"
+                       (string-append "LDC_LIB_PATH="
                                              (assoc-ref inputs "ldc")
                                              "/lib")))))
            (replace
@@ -435,3 +664,132 @@ supported.")
     (description
      "FastQC aims to provide a QC report which can spot problems which originate either in the sequencer or in the starting library material. It can either run as a stand alone interactive application for the immediate analysis of small numbers of FastQ files, or it can be run in a non-interactive mode where it would be suitable for integrating into a larger analysis pipeline for the systematic processing of large numbers of files.")
     (license license:gpl3+)))
+
+(define-public vcflib
+  (let ((commit "3ce827d8ebf89bb3bdc097ee0fe7f46f9f30d5fb"))
+    (package
+      (name "vcflib")
+      (version (string-append "v1.0.2-" (string-take commit 7)))
+      (source
+       (origin
+         (method url-fetch)
+         (uri (string-append "https://github.com/vcflib/vcflib/archive/"
+                "5ac091365fdc716cc47cc5410bb97ee5dc2a2c92" ".tar.gz"))
+         (file-name "vcflib-5ac0913.tar.gz")
+         (sha256
+          (base32 "0ywshwpif059z5h0g7zzrdfzzdj2gr8xvwlwcsdxrms3p9iy35h8"))))
+      (build-system gnu-build-system)
+      (native-inputs
+       `(("htslib" ,htslib)
+         ("zlib" ,zlib)
+         ("python" ,python-2)
+         ("perl" ,perl)
+         ("tabixpp-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/tabixpp/archive/"
+                  "bbc63a49acc52212199f92e9e3b8fba0a593e3f7" ".tar.gz"))
+            (file-name "tabixpp-src.tar.gz")
+            (sha256
+             (base32 "1s06wmpgj4my4pik5kp2lc42hzzazbp5ism2y4i2ajp2y1c68g77"))))
+         ("intervaltree-src"
+          ,(origin
+             (method url-fetch)
+             (uri (string-append
+                   "https://github.com/ekg/intervaltree/archive/"
+                   "dbb4c513d1ad3baac516fc1484c995daf9b42838" ".tar.gz"))
+             (file-name "intervaltree-src.tar.gz")
+             (sha256
+              (base32 "19prwpn2wxsrijp5svfqvfcxl5nj7zdhm3jycd5kqhl9nifpmcks"))))
+         ("smithwaterman-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/smithwaterman/archive/"
+                  "203218b47d45ac56ef234716f1bd4c741b289be1" ".tar.gz"))
+            (file-name "smithwaterman-src.tar.gz")
+            (sha256
+             (base32 "1lkxy4xkjn96l70jdbsrlm687jhisgw4il0xr2dm33qwcclzzm3b"))))
+         ("multichoose-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/multichoose/archive/"
+                  "73d35daa18bf35729b9ba758041a9247a72484a5" ".tar.gz"))
+            (file-name "multichoose-src.tar.gz")
+            (sha256
+             (base32 "07aizwdabmlnjaq4p3v0vsasgz1xzxid8xcxcw3paq8kh9c1099i"))))
+         ("fsom-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/fsom/archive/"
+                  "a6ef318fbd347c53189384aef7f670c0e6ce89a3" ".tar.gz"))
+            (file-name "fsom-src.tar.gz")
+            (sha256
+             (base32 "0q6b57ppxfvsm5cqmmbfmjpn5qvx2zi5pamvp3yh8gpmmz8cfbl3"))))
+         ("filevercmp-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/filevercmp/archive/"
+                  "1a9b779b93d0b244040274794d402106907b71b7" ".tar.gz"))
+            (file-name "filevercmp-src.tar.gz")
+            (sha256
+             (base32 "0yp5jswf5j2pqc6517x277s4s6h1ss99v57kxw9gy0jkfl3yh450"))))
+         ("fastahack-src"
+          ,(origin
+            (method url-fetch)
+            (uri (string-append "https://github.com/ekg/fastahack/archive/"
+                  "c68cebb4f2e5d5d2b70cf08fbdf1944e9ab2c2dd" ".tar.gz"))
+            (file-name "fastahack-src.tar.gz")
+            (sha256
+             (base32 "0j25lcl3jk1kls66zzxjfyq5ir6sfcvqrdwfcva61y3ajc9ssay2"))))))
+      (arguments
+       `(#:tests? #f
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'configure)
+           (delete 'check)
+           (add-after 'unpack 'unpack-submodule-sources
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let ((unpack (lambda (source target)
+                               (with-directory-excursion target
+                                 (zero? (system* "tar" "xvf"
+                                        (assoc-ref inputs source)
+                                        "--strip-components=1"))))))
+                 (and
+                  (unpack "intervaltree-src" "intervaltree")
+                  (unpack "fastahack-src" "fastahack")
+                  (unpack "filevercmp-src" "filevercmp")
+                  (unpack "fsom-src" "fsom")
+                  (unpack "intervaltree-src" "intervaltree")
+                  (unpack "multichoose-src" "multichoose")
+                  (unpack "smithwaterman-src" "smithwaterman")
+                  (unpack "tabixpp-src" "tabixpp")))))
+           (add-after 'unpack-submodule-sources 'fix-makefile
+             (lambda* (#:key inputs #:allow-other-keys)
+               (substitute* '("Makefile")
+                 (("^GIT_VERSION.*") "GIT_VERSION = v1.0.0"))))
+           (replace
+            'build
+            (lambda* (#:key inputs make-flags #:allow-other-keys)
+              (with-directory-excursion "tabixpp"
+                (zero? (system* "make")))
+              (zero? (system* "make" "CC=gcc"
+                (string-append "CFLAGS=\"" "-Itabixpp "
+                  "-I" (assoc-ref inputs "htslib") "/include " "\"") "all"))))
+           (replace
+            'install
+            (lambda* (#:key outputs #:allow-other-keys)
+              (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+                    (lib (string-append (assoc-ref outputs "out") "/lib")))
+                (for-each (lambda (file)
+                           (install-file file bin))
+                         (find-files "bin" ".*"))
+                (install-file "libvcflib.a" lib)))))))
+      (home-page "https://github.com/vcflib/vcflib/")
+      (synopsis "Library for parsing and manipulating VCF files")
+      (description "Vcflib provides methods to manipulate and interpret
+sequence variation as it can be described by VCF. It is both an API for parsing
+and operating on records of genomic variation as it can be described by the VCF
+format, and a collection of command-line utilities for executing complex
+manipulations on VCF files.")
+      (license license:expat))))
+
diff --git a/gn/packages/genenetwork.scm b/gn/packages/genenetwork.scm
index aec305b..fdcbb7f 100644
--- a/gn/packages/genenetwork.scm
+++ b/gn/packages/genenetwork.scm
@@ -87,7 +87,6 @@
     (description #f)
     (license #f)))
 
-
 (define-public genenetwork1
   (let ((commit "d622c803b"))
   (package
@@ -141,7 +140,7 @@
     (license license:agpl3+))))
 
 (define-public genenetwork2
-  (let ((commit "8c9de7e5a2016f1e5b7397be1a8e84396e3a25c5"))
+  (let ((commit "a8fcff44d3bd768d02e7ed0c80b84d2516bdad2a"))
   (package
     (name "genenetwork2")
     (version (string-append "2.0-" (string-take commit 7) ))
@@ -149,12 +148,12 @@
              (method git-fetch)
              (uri (git-reference
                    ;; (url "https://github.com/genenetwork/genenetwork2.git")
-                   (url "https://github.com/pjotrp/genenetwork2.git")
+                   (url "https://github.com/genenetwork/genenetwork2_diet.git")
                    (commit commit)))
              (file-name (string-append name "-" (string-take commit 7))) 
              (sha256
               (base32
-               "1kgigzs4rs6zgbqbnm40rcljzz9prlwv7n2n9an57jk58bjgf6v8"))))
+               "1zs6jgrpwzxmfjz03whnaw8q6h8f53mycl440p058gfn8x7pd618"))))
     (propagated-inputs `(  ;; propagated for development purposes
               ("python" ,python-2) ;; probably superfluous
               ("r" ,r)
@@ -162,6 +161,7 @@
               ("redis" ,redis)
               ("mysql" ,mysql)
               ("gemma" ,gemma-git)
+              ("genenetwork2-files-small" ,genenetwork2-files-small)
               ("pylmm-gn2" ,pylmm-gn2)
               ("plink2" ,plink-ng)
               ("nginx" ,nginx)
@@ -195,6 +195,13 @@
     (build-system python-build-system)
     (arguments
      `(#:python ,python-2
+       #:phases
+         (modify-phases %standard-phases
+           (add-before 'install 'fix-paths
+             (lambda* (#:key inputs #:allow-other-keys)
+               (let* ((datafiles (string-append (assoc-ref inputs "genenetwork2-files-small") "/share/genenetwork2" )))
+               (substitute* '("etc/default_settings.py")
+                 (("^GENENETWORK_FILES =.*") (string-append "GENENETWORK_FILES = \"" datafiles "\"\n" )))))))
        #:tests? #f))   ; no 'setup.py test'
     (home-page "http://genenetwork.org/")
     (synopsis "Full genenetwork services")
@@ -204,6 +211,48 @@
 ;; ./pre-inst-env guix download http://files.genenetwork.org/raw_database/db_webqtl_s.zip
 ;; 0sscjh0wml2lx0mb43vf4chg9gpbfi7abpjxb34n3kyny9ll557x
 
+(define-public genenetwork2-files-small
+  (let ((pfff "xx"))
+    (package
+    (name "genenetwork2-files-small")
+    (version "1.0")
+    (source
+     (origin
+       (method url-fetch)
+       (uri "http://files.genenetwork.org/data_files/gn2_data_s-20160303-C9E672ECED1F51B915DE419B5B2C524E.tar.lz4")
+       (file-name (string-append name "-" pfff)) 
+       (sha256
+        (base32 "058ymx3af6abdhdxyxj0i9qfvb6v7j091frjpp6jh4ahks7r23lj"))))
+    (build-system trivial-build-system)
+    (native-inputs `(("lz4" ,lz4)
+                     ("tar" ,tar)
+                     ("source" ,source)))
+
+    (arguments
+     `(#:modules ((guix build utils))
+       #:builder
+       (let* ((out (assoc-ref %outputs "out"))
+              (name "gn2_data_s")
+              (tarfn (string-append name ".tar"))
+              (targetdir (string-append out "/share/genenetwork2/"))
+              )
+           (begin
+             (use-modules (guix build utils))
+             (let ((source (assoc-ref %build-inputs "source"))
+                   (lz4unpack (string-append (assoc-ref %build-inputs "lz4") "/bin/lz4"))
+                   (tar (string-append (assoc-ref %build-inputs "tar") "/bin/tar"))
+                   )
+               (and 
+                    (zero? (system* lz4unpack source "-d" tarfn))
+                    (zero? (system* tar "xf" tarfn))
+                    (mkdir-p targetdir)
+                    (copy-recursively name targetdir)
+                    ))))))
+    (home-page "http://genenetwork.org/")
+    (synopsis "Small file archive to run on genenetwork")
+    (description "Genenetwork genotype and mapping files.")
+    (license license:agpl3+))))
+
 (define-public genenetwork2-database-small
   (let ((md5 "93e745e9c"))
     (package
diff --git a/gn/packages/python.scm b/gn/packages/python.scm
index 7781521..6fff9a3 100644
--- a/gn/packages/python.scm
+++ b/gn/packages/python.scm
@@ -279,16 +279,14 @@ powerful language for representing information.")
         (base32
           "06qzgwk7j66k8ggx51i6wxx0f0zsppp7w4bh6gjd0cr9rfs86jn7"))))
   (build-system python-build-system)
-  (inputs
+  (propagated-inputs
    `(
      ("mysql" ,mysql)
      ("python-nose" ,python-nose)
      ("zlib" ,zlib)
      ("openssl" ,openssl)
      ("libgcrypt" ,libgcrypt)
-     ))
-  (propagated-inputs
-   `(("python-setuptools" ,python-setuptools)
+     ("python-setuptools" ,python-setuptools)
      ))
   (arguments
    `(#:tests? #f))   ; wants a running MySQL server
generated by cgit-pink 1.4.1 (git 2.36.1) at 2025-10-06 22:28:05 +0000