bioinformatics: Remove kraken2.

It is available in the main Guix repository.

* guix-science/packages/bioinformatics.scm (kraken2): Remove variable.
* kraken2-fix-link-error.patch: Remove file.

2 files changed, 0 insertions, 87 deletions

diff --git a/guix-science/packages/bioinformatics.scm b/guix-science/packages/bioinformatics.scm
index 62bb6ac..3318268 100644
--- a/guix-science/packages/bioinformatics.scm
+++ b/guix-science/packages/bioinformatics.scm
@@ -300,62 +300,6 @@ data.  For whole genome sequencing data analysis, the program can also use
 mappability data (files created by GEM).")
     (license license:gpl2+)))
 
-(define-public kraken2
-  (package
-   (name "kraken2")
-   (version "2.1.1")
-   (source (origin
-                  (method url-fetch)
-                  (uri "https://github.com/DerrickWood/kraken2/archive/v2.1.1.tar.gz")
-                  (file-name (string-append name "-" version ".tar.gz"))
-                  (sha256
-                   (base32 "1r6yh6df2rg42s6kxxih7zyabcjp2lyp0i2vypkfif9jvf694glg"))
-                  (patches (list (search-patch "kraken2-fix-link-error.patch")))))
-   (build-system cmake-build-system)
-   (arguments
-    `(#:tests? #f
-      #:phases
-      (modify-phases %standard-phases
-        (replace 'install
-                (lambda* (#:key inputs outputs #:allow-other-keys)
-                  (let* ((out           (assoc-ref outputs "out"))
-                               (bin           (string-append out "/bin"))
-                               (wget          (string-append (assoc-ref inputs "wget") "/bin/wget"))
-                               (rsync         (string-append (assoc-ref inputs "rsync") "/bin/rsync"))
-                               (local-scripts (string-append "../" ,name "-" ,version "/scripts")))
-                    (with-directory-excursion local-scripts
-                      (substitute* '("download_taxonomy.sh"
-                                                 "download_genomic_library.sh"
-                                                 "rsync_from_ncbi.pl")
-                                         (("rsync -") (string-append rsync " -")))
-                            (substitute* '("16S_gg_installation.sh"
-                                                 "16S_rdp_installation.sh"
-                                                 "16S_silva_installation.sh"
-                                                 "download_genomic_library.sh"
-                                                 "download_taxonomy.sh")
-                                         (("wget ") (string-append wget " "))))
-
-                    (copy-recursively local-scripts bin)
-                    (with-directory-excursion "src"
-                            (for-each (lambda (file) (install-file file bin))
-                                            '("build_db"
-                                              "classify"
-                                              "dump_table"
-                                              "estimate_capacity"
-                                              "lookup_accession_numbers"))))
-                  #t)))))
-   (native-inputs
-    `(("gcc" ,gcc-10)))
-   (inputs
-    `(("perl" ,perl)
-      ("rsync" ,rsync)
-      ("wget" ,wget)))
-   (home-page "https://github.com/DerrickWood/kraken2")
-   (synopsis "Taxonomic sequence classification system")
-   (description "Kraken is an ultrafast and highly accurate program for
-assigning taxonomic labels to metagenomic DNA sequences.")
-   (license license:expat)))
-
 (define-public python-pyvcf
   (package
     (name "python-pyvcf")
diff --git a/kraken2-fix-link-error.patch b/kraken2-fix-link-error.patch
deleted file mode 100644
index aea1ad1..0000000
--- a/kraken2-fix-link-error.patch
+++ /dev/null
@@ -1,31 +0,0 @@
-From 9fca31e2becbeb90c527b89812fbc6f6ff2f3959 Mon Sep 17 00:00:00 2001
-From: starling13 <starling13@mail.ru>
-Date: Fri, 25 Dec 2020 13:09:05 +0300
-Subject: [PATCH] Fix link issue with using cmake
-
----
- src/CMakeLists.txt | 4 +++-
- 1 file changed, 3 insertions(+), 1 deletion(-)
-
-diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
-index 928ceba..bb76dd3 100644
---- a/src/CMakeLists.txt
-+++ b/src/CMakeLists.txt
-@@ -11,6 +11,7 @@ add_executable(build_db
- add_executable(classify
-         classify.cc
-         reports.cc
-+        hyperloglogplus.cc
-         mmap_file.cc
-         compact_hash.cc
-         taxonomy.cc
-@@ -33,7 +34,8 @@ add_executable(dump_table
-         compact_hash.cc
-         omp_hack.cc
-         taxonomy.cc
--        reports.cc)
-+        reports.cc
-+        hyperloglogplus.cc)
- 
- add_executable(lookup_accession_numbers
-         lookup_accession_numbers.cc