[bug#40086] [PATCH 00/11] Expand edirect programs

[bug#40086] [PATCH 00/11] Expand edirect programs

[Efraim Flashner]

There are a lot more programs and pieces to edirect and I've had these
in a separate channel for a while. It would certainly be far more
convenient to have this upstream in Guix itself.

Efraim Flashner (11):
  gnu: Add go-golang-org-x-image.
  gnu: Add go-golang-org-rainycape-unidecode.
  gnu: Add go-github-com-golang-freetype.
  gnu: Add go-github-com-fogleman-gg.
  gnu: Add go-github-com-gedex-inflector.
  gnu: Add go-github-com-klauspost-cpuid.
  gnu: Add go-github-com-pbnjay-memory.
  gnu: Add go-github-com-surge-glog.
  gnu: Add go-github-com-surgebase-porter2.
  gnu: Add edirect-go-programs.
  gnu: edirect: Install more programs.

 gnu/packages/bioinformatics.scm | 114 +++++++++++++--
 gnu/packages/golang.scm         | 237 +++++++++++++++++++++++++++++++-
 2 files changed, 337 insertions(+), 14 deletions(-)

-- 
2.25.1

[bug#40086] [PATCH 01/11] gnu: Add go-golang-org-x-image.

[Efraim Flashner]

* gnu/packages/golang.scm (go-golang-org-x-image): New variable.
---
 gnu/packages/golang.scm | 32 +++++++++++++++++++++++++++++++-
 1 file changed, 31 insertions(+), 1 deletion(-)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 0d92139311..782709fdf6 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -1,5 +1,5 @@
 ;;; GNU Guix --- Functional package management for GNU
-;;; Copyright © 2016, 2017, 2018, 2019 Efraim Flashner <efraim@flashner.co.il>
+;;; Copyright © 2016, 2017, 2018, 2019, 2020 Efraim Flashner <efraim@flashner.co.il>
 ;;; Copyright © 2016 Matthew Jordan <matthewjordandevops@yandex.com>
 ;;; Copyright © 2016 Andy Wingo <wingo@igalia.com>
 ;;; Copyright © 2016, 2019 Ludovic Courtès <ludo@gnu.org>
@@ -692,6 +692,36 @@ for the Go language.")
       (home-page "https://go.googlesource.com/net")
       (license license:bsd-3))))
 
+(define-public go-golang-org-x-image
+  (let ((commit "58c23975cae11f062d4b3b0c143fe248faac195d")
+        (revision "1"))
+    (package
+      (name "go-golang-org-x-image")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://go.googlesource.com/image")
+                       (commit commit)))
+                (file-name (string-append "go.googlesource.com-image-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "0i2p2girc1sfcic6xs6vrq0fp3szfx057xppksb67kliywjjrm5x"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "golang.org/x/image"
+         ; Source-only package
+         #:tests? #f
+         #:phases
+         (modify-phases %standard-phases
+           (delete 'build))))
+      (home-page "https://go.googlesource.com/image")
+      (synopsis "Supplemental Go image libraries")
+      (description "This package provides supplemental Go libraries for image
+processing.")
+      (license license:bsd-3))))
+
 (define-public go-golang-org-x-sys
   (let ((commit "749cb33beabd9aa6d3178e3de05bcc914f70b2bf")
         (revision "5"))
-- 
2.25.1

[bug#40086] [PATCH 02/11] gnu: Add go-golang-org-rainycape-unidecode.

[Efraim Flashner]

* gnu/packages/golang.scm (go-golang-org-rainycape-unidecode): New variable.
---
 gnu/packages/golang.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 782709fdf6..db40973063 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -3426,3 +3426,28 @@ data serialization format.")
     (description " A glob library that implements descending into other
 directories.  It is optimized for filewalking. ")
     (license license:expat)))
+
+(define-public go-golang-org-rainycape-unidecode
+  (let ((commit "cb7f23ec59bec0d61b19c56cd88cee3d0cc1870c")
+        (revision "1"))
+    (package
+      (name "go-golang-org-rainycape-unidecode")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/rainycape/unidecode")
+                       (commit commit)))
+                (file-name (string-append "go-golang-org-rainycape-unidecode-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "1wvzdijd640blwkgmw6h09frkfa04kcpdq87n2zh2ymj1dzla5v5"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "golang.org/rainycape/unidecode"))
+      (home-page "https://github.com/rainycape/unidecode")
+      (synopsis "Unicode transliterator in Golang")
+      (description "Unicode transliterator in Golang - Replaces non-ASCII
+characters with their ASCII approximations.")
+      (license license:asl2.0))))
-- 
2.25.1

[bug#40086] [PATCH 03/11] gnu: Add go-github-com-golang-freetype.

[Efraim Flashner]

* gnu/packages/golang.scm (go-github-com-golang-freetype): New variable.
---
 gnu/packages/golang.scm | 27 +++++++++++++++++++++++++++
 1 file changed, 27 insertions(+)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index db40973063..5de4f8f635 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -3451,3 +3451,30 @@ directories.  It is optimized for filewalking. ")
       (description "Unicode transliterator in Golang - Replaces non-ASCII
 characters with their ASCII approximations.")
       (license license:asl2.0))))
+
+(define-public go-github-com-golang-freetype
+  (let ((commit "e2365dfdc4a05e4b8299a783240d4a7d5a65d4e4")
+        (revision "1"))
+    (package
+      (name "go-github-com-golang-freetype")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/golang/freetype")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-golang-freetype-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "194w3djc6fv1rgcjqds085b9fq074panc5vw582bcb8dbfzsrqxc"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/golang/freetype"))
+      (propagated-inputs
+       `(("go-golang-org-x-image" ,go-golang-org-x-image)))
+      (home-page "https://github.com/golang/freetype")
+      (synopsis "Freetype font rasterizer in the Go programming language")
+      (description "The Freetype font rasterizer in the Go programming language.")
+      (license (list license:freetype
+                     license:gpl2+)))))
-- 
2.25.1

[bug#40086] [PATCH 04/11] gnu: Add go-github-com-fogleman-gg.

[Efraim Flashner]

* gnu/packages/golang.scm (go-github-com-fogleman-gg): New variable.
---
 gnu/packages/golang.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 5de4f8f635..64e226e03a 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -3478,3 +3478,27 @@ characters with their ASCII approximations.")
       (description "The Freetype font rasterizer in the Go programming language.")
       (license (list license:freetype
                      license:gpl2+)))))
+
+(define-public go-github-com-fogleman-gg
+  (package
+    (name "go-github-com-fogleman-gg")
+    (version "1.3.0")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/fogleman/gg")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1nkldjghbqnzj2djfaxhiv35kk341xhcrj9m2dwq65v684iqkk8n"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:tests? #f      ; Issue with test flags.
+       #:import-path "github.com/fogleman/gg"))
+    (propagated-inputs
+     `(("go-github-com-golang-freetype" ,go-github-com-golang-freetype)))
+    (home-page "https://github.com/fogleman/gg")
+    (synopsis "2D rendering in Go")
+    (description "@code{gg} is a library for rendering 2D graphics in pure Go.")
+    (license license:expat)))
-- 
2.25.1

[bug#40086] [PATCH 05/11] gnu: Add go-github-com-gedex-inflector.

[Efraim Flashner]

* gnu/packages/golang.scm (go-github-com-gedex-inflector): New variable.
---
 gnu/packages/golang.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 64e226e03a..419b88552a 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -3502,3 +3502,27 @@ characters with their ASCII approximations.")
     (synopsis "2D rendering in Go")
     (description "@code{gg} is a library for rendering 2D graphics in pure Go.")
     (license license:expat)))
+
+(define-public go-github-com-gedex-inflector
+  (let ((commit "16278e9db8130ac7ec405dc174cfb94344f16325")
+        (revision "1"))
+    (package
+      (name "go-github-com-gedex-inflector")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/gedex/inflector")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-gedex-inflector-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "05hjqw1m71vww4914d9h6nqa9jw3lgjzwsy7qaffl02s2lh1amks"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/gedex/inflector"))
+      (home-page "https://github.com/gedex/inflector")
+      (synopsis "Go library that pluralizes and singularizes English nouns")
+      (description "Go library that pluralizes and singularizes English nouns.")
+      (license license:bsd-2))))
-- 
2.25.1

[bug#40086] [PATCH 06/11] gnu: Add go-github-com-klauspost-cpuid.

[Efraim Flashner]

* gnu/packages/golang.scm (go-github-com-klauspost-cpuid): New variable.
---
 gnu/packages/golang.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 419b88552a..11dfb23e46 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -3526,3 +3526,28 @@ characters with their ASCII approximations.")
       (synopsis "Go library that pluralizes and singularizes English nouns")
       (description "Go library that pluralizes and singularizes English nouns.")
       (license license:bsd-2))))
+
+(define-public go-github-com-klauspost-cpuid
+  (package
+    (name "go-github-com-klauspost-cpuid")
+    (version "1.2.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/klauspost/cpuid")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1s510210wdj5dkamii1qrk7v87k4qpdcrrjzflp5ha9iscw6b06l"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/klauspost/cpuid"))
+    (home-page "https://github.com/klauspost/cpuid")
+    (synopsis "CPU feature identification for Go")
+    (description "@code{cpuid} provides information about the CPU running the
+current program.  CPU features are detected on startup, and kept for fast access
+through the life of the application. Currently x86 / x64 (AMD64) is supported,
+and no external C (cgo) code is used, which should make the library very eas
+to use.")
+    (license license:expat)))
-- 
2.25.1

[bug#40086] [PATCH 06/11] gnu: Add go-github-com-klauspost-cpuid.

[Efraim Flashner]

* gnu/packages/golang.scm (go-github-com-klauspost-cpuid): New variable.
---
 gnu/packages/golang.scm | 25 +++++++++++++++++++++++++
 1 file changed, 25 insertions(+)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 419b88552a..11dfb23e46 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -3526,3 +3526,28 @@ characters with their ASCII approximations.")
       (synopsis "Go library that pluralizes and singularizes English nouns")
       (description "Go library that pluralizes and singularizes English nouns.")
       (license license:bsd-2))))
+
+(define-public go-github-com-klauspost-cpuid
+  (package
+    (name "go-github-com-klauspost-cpuid")
+    (version "1.2.3")
+    (source (origin
+              (method git-fetch)
+              (uri (git-reference
+                     (url "https://github.com/klauspost/cpuid")
+                     (commit (string-append "v" version))))
+              (file-name (git-file-name name version))
+              (sha256
+               (base32
+                "1s510210wdj5dkamii1qrk7v87k4qpdcrrjzflp5ha9iscw6b06l"))))
+    (build-system go-build-system)
+    (arguments
+     `(#:import-path "github.com/klauspost/cpuid"))
+    (home-page "https://github.com/klauspost/cpuid")
+    (synopsis "CPU feature identification for Go")
+    (description "@code{cpuid} provides information about the CPU running the
+current program.  CPU features are detected on startup, and kept for fast access
+through the life of the application. Currently x86 / x64 (AMD64) is supported,
+and no external C (cgo) code is used, which should make the library very eas
+to use.")
+    (license license:expat)))
-- 
2.25.1

[bug#40086] [PATCH 07/11] gnu: Add go-github-com-pbnjay-memory.

[Efraim Flashner]

* gnu/packages/golang.scm (go-github-com-pbnjay-memory): New variable.
---
 gnu/packages/golang.scm | 26 ++++++++++++++++++++++++++
 1 file changed, 26 insertions(+)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 11dfb23e46..30e4b4147f 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -3551,3 +3551,29 @@ through the life of the application. Currently x86 / x64 (AMD64) is supported,
 and no external C (cgo) code is used, which should make the library very eas
 to use.")
     (license license:expat)))
+
+(define-public go-github-com-pbnjay-memory
+  (let ((commit "974d429e7ae40c89e7dcd41cfcc22a0bfbe42510")
+        (revision "1"))
+    (package
+      (name "go-github-com-pbnjay-memory")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/pbnjay/memory")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-pbnjay-memory-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "0kazg5psdn90pqadrzma5chdwh0l2by9z31sspr47gx93fhjmkkq"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/pbnjay/memory"))
+      (home-page "https://github.com/gedex/inflector")
+      (synopsis "Go library to report total system memory")
+      (description "@code{memory} provides a single method reporting total
+physical system memory accessible to the kernel. It does not account for memory
+used by other processes.")
+      (license license:bsd-3))))
-- 
2.25.1

[bug#40086] [PATCH 08/11] gnu: Add go-github-com-surge-glog.

[Efraim Flashner]

* gnu/packages/golang.scm (go-github-com-surge-glog): New variable.
---
 gnu/packages/golang.scm | 24 ++++++++++++++++++++++++
 1 file changed, 24 insertions(+)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 30e4b4147f..6b09dcbe58 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -3577,3 +3577,27 @@ to use.")
 physical system memory accessible to the kernel. It does not account for memory
 used by other processes.")
       (license license:bsd-3))))
+
+(define-public go-github-com-surge-glog
+  (let ((commit "2578deb2b95c665e6b1ebabf304ce2085c9e1985")
+        (revision "1"))
+    (package
+      (name "go-github-com-surge-glog")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/surge/glog")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-surge-glog-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "1bxcwxvsvr2hfpjz9hrrn0wrgykwmrbyk567102k3vafw9xdcwk4"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/surge/glog"))
+      (home-page "https://github.com/surge/glog")
+      (synopsis "Leveled execution logs for Go")
+      (description "Leveled execution logs for Go.")
+      (license license:asl2.0))))
-- 
2.25.1

[bug#40086] [PATCH 09/11] gnu: Add go-github-com-surgebase-porter2.

[Efraim Flashner]

* gnu/packages/golang.scm (go-github-com-surgebase-porter2): New variable.
---
 gnu/packages/golang.scm | 30 ++++++++++++++++++++++++++++++
 1 file changed, 30 insertions(+)

diff --git a/gnu/packages/golang.scm b/gnu/packages/golang.scm
index 6b09dcbe58..0e1d2dc22a 100644
--- a/gnu/packages/golang.scm
+++ b/gnu/packages/golang.scm
@@ -3601,3 +3601,33 @@ used by other processes.")
       (synopsis "Leveled execution logs for Go")
       (description "Leveled execution logs for Go.")
       (license license:asl2.0))))
+
+(define-public go-github-com-surgebase-porter2
+  (let ((commit "56e4718818e8dc4ea5ba6348402fc7661863732a")
+        (revision "1"))
+    (package
+      (name "go-github-com-surgebase-porter2")
+      (version (git-version "0.0.0" revision commit))
+      (source (origin
+                (method git-fetch)
+                (uri (git-reference
+                       (url "https://github.com/surgebase/porter2")
+                       (commit commit)))
+                (file-name (string-append "go-github-com-surgebase-porter2-"
+                                          version "-checkout"))
+                (sha256
+                 (base32
+                  "1ivcf83jlj9s7q5y9dfbpyl0br35cz8fcp0dm8sxxvqh54py06v2"))))
+      (build-system go-build-system)
+      (arguments
+       `(#:import-path "github.com/surgebase/porter2"))
+      (native-inputs
+       `(("go-github-com-stretchr-testify" ,go-github-com-stretchr-testify)
+         ("go-github-com-surge-glog" ,go-github-com-surge-glog)))
+      (home-page "https://github.com/surgebase/porter2")
+      (synopsis "Go library implementing english Porter2 stemmer")
+      (description "Porter2 implements the
+@url{http://snowball.tartarus.org/algorithms/english/stemmer.html, english
+Porter2 stemmer}.  It is written completely using finite state machines to do
+suffix comparison, rather than the string-based or tree-based approaches.")
+      (license license:asl2.0))))
-- 
2.25.1

[bug#40086] [PATCH 10/11] gnu: Add edirect-go-programs.

[Efraim Flashner]

* gnu/packages/bioinformatics.scm (edirect-go-programs): New variable.
(edirect)[source]: Adjust snippet to not use non-free software.
---
 gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++++++--
 1 file changed, 54 insertions(+), 3 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 4dedee6223..1f0619ebb6 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -42,6 +42,7 @@
   #:use-module (guix build-system ant)
   #:use-module (guix build-system gnu)
   #:use-module (guix build-system cmake)
+  #:use-module (guix build-system go)
   #:use-module (guix build-system haskell)
   #:use-module (guix build-system meson)
   #:use-module (guix build-system ocaml)
@@ -68,15 +69,17 @@
   #:use-module (gnu packages documentation)
   #:use-module (gnu packages databases)
   #:use-module (gnu packages datastructures)
+  #:use-module (gnu packages dlang)
   #:use-module (gnu packages file)
   #:use-module (gnu packages flex)
   #:use-module (gnu packages gawk)
   #:use-module (gnu packages gcc)
   #:use-module (gnu packages gd)
-  #:use-module (gnu packages gtk)
+  #:use-module (gnu packages golang)
   #:use-module (gnu packages glib)
   #:use-module (gnu packages graph)
   #:use-module (gnu packages groff)
+  #:use-module (gnu packages gtk)
   #:use-module (gnu packages guile)
   #:use-module (gnu packages guile-xyz)
   #:use-module (gnu packages haskell-check)
@@ -87,7 +90,6 @@
   #:use-module (gnu packages java)
   #:use-module (gnu packages java-compression)
   #:use-module (gnu packages jemalloc)
-  #:use-module (gnu packages dlang)
   #:use-module (gnu packages linux)
   #:use-module (gnu packages lisp-xyz)
   #:use-module (gnu packages logging)
@@ -2766,7 +2768,12 @@ quantitative phenotypes.")
                 "093zp7klv81ph0y8mm8d78a9hnpfxbv2kdym70gzdf3vz176rw33"))
               (modules '((guix build utils)))
               (snippet
-               '(begin (delete-file "Mozilla-CA.tar.gz") #t))))
+               '(begin (delete-file "Mozilla-CA.tar.gz")
+                       (substitute* "rchive.go"
+                         ;; This go library does not have any license.
+                         (("github.com/fiam/gounidecode/unidecode")
+                          "golang.org/rainycape/unidecode"))
+                       #t))))
     (build-system perl-build-system)
     (arguments
      `(#:phases
@@ -2826,6 +2833,50 @@ in structured XML format.  This can eliminate the need for writing custom
 software to answer ad hoc questions.")
     (license license:public-domain)))
 
+(define-public edirect-go-programs
+  (package
+    (inherit edirect)
+    (name "edirect-go-programs")
+    (build-system go-build-system)
+    (arguments
+     `(#:install-source? #f
+       #:tests? #f      ; No tests.
+       #:import-path "ncbi.nlm.nih.gov/entrez/edirect"
+       #:phases
+       (modify-phases %standard-phases
+         (replace 'build
+           (lambda* (#:key import-path #:allow-other-keys)
+             (with-directory-excursion (string-append "src/" import-path)
+               (invoke "go" "build" "-v" "-x" "j2x.go")
+               (invoke "go" "build" "-v" "-x" "t2x.go")
+               (invoke "go" "build" "-v" "-x" "-o"
+                       "xtract.Linux" "xtract.go" "common.go")
+               (invoke "go" "build" "-v" "-x" "-o"
+                       "rchive.Linux" "rchive.go" "common.go")
+               (invoke "go" "build" "-v" "-x" "-o" "symbols.Linux" "s2p.go"))))
+         (replace 'install
+           (lambda* (#:key outputs import-path #:allow-other-keys)
+             (let ((dest    (string-append (assoc-ref outputs "out") "/bin"))
+                   (source  (string-append "src/" import-path "/")))
+               (for-each (lambda (file)
+                           (format #t "installing ~a~%" file)
+                           (install-file (string-append source file) dest))
+                         '("j2x" "t2x" "symbols.Linux" "xtract.Linux" "rchive.Linux"))
+               #t))))))
+    (native-inputs '())
+    (propagated-inputs '())
+    (inputs
+     `(("go-github-com-fatih-color" ,go-github-com-fatih-color)
+       ("go-github-com-fogleman-gg" ,go-github-com-fogleman-gg)
+       ("go-github-com-gedex-inflector" ,go-github-com-gedex-inflector)
+       ("go-github-com-golang-freetype" ,go-github-com-golang-freetype)
+       ("go-github-com-klauspost-cpuid" ,go-github-com-klauspost-cpuid)
+       ("go-github-com-pbnjay-memory" ,go-github-com-pbnjay-memory)
+       ("go-github-com-surgebase-porter2" ,go-github-com-surgebase-porter2)
+       ("go-golang-org-rainycape-unidecode" ,go-golang-org-rainycape-unidecode)
+       ("go-golang-org-x-image" ,go-golang-org-x-image)
+       ("go-golang-org-x-text" ,go-golang-org-x-text)))))
+
 (define-public exonerate
   (package
     (name "exonerate")
-- 
2.25.1

[bug#40086] [PATCH 11/11] gnu: edirect: Install more programs.

[Efraim Flashner]

* gnu/packages/bioinformatics.scm (edirect)[arguments]: Add
'patch-programs phase to work around not finding binaries in the PATH.
Rewrite 'install phase to install many more scripts. Rewrite
'wrap-program to wrap more scripts with more programs.
[inputs]: Add edirect-go-programs.
[native-search-paths]: New field.
---
 gnu/packages/bioinformatics.scm | 57 +++++++++++++++++++++++++++------
 1 file changed, 47 insertions(+), 10 deletions(-)

diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm
index 1f0619ebb6..da36733412 100644
--- a/gnu/packages/bioinformatics.scm
+++ b/gnu/packages/bioinformatics.scm
@@ -2781,19 +2781,48 @@ quantitative phenotypes.")
          (delete 'configure)
          (delete 'build)
          (delete 'check)                ; simple check after install
+         (add-after 'unpack 'patch-programs
+           (lambda* (#:key inputs #:allow-other-keys)
+             ;; Ignore errors about missing xtract.Linux and rchive.Linux.
+              (substitute* "pm-refresh"
+                (("cat \\\"\\$target")
+                 "grep ^[[:digit:]] \"$target"))
+              #t))
          (replace 'install
-           (lambda* (#:key outputs #:allow-other-keys)
-             (install-file "edirect.pl"
-                           (string-append (assoc-ref outputs "out") "/bin"))
-             #t))
+            (lambda* (#:key inputs outputs #:allow-other-keys)
+              (let ((bin (string-append (assoc-ref outputs "out") "/bin"))
+                    (edirect-go (assoc-ref inputs "edirect-go-programs")))
+                (for-each
+                  (lambda (file)
+                    (install-file file bin))
+                  '("archive-pubmed" "asp-cp" "asp-ls" "download-ncbi-data"
+                    "download-pubmed" "edirect.pl" "efetch" "epost" "esearch"
+                    "fetch-pubmed" "ftp-cp" "ftp-ls" "has-asp" "index-pubmed"
+                    "pm-prepare" "pm-refresh" "pm-stash" "pm-collect"
+                    "pm-index" "pm-invert" "pm-merge" "pm-promote"))
+                (symlink (string-append edirect-go "/bin/xtract.Linux")
+                         (string-append bin "/xtract"))
+                (symlink (string-append edirect-go "/bin/rchive.Linux")
+                         (string-append bin "/rchive")))
+              #t))
          (add-after 'install 'wrap-program
            (lambda* (#:key outputs #:allow-other-keys)
-             ;; Make sure 'edirect.pl' finds all perl inputs at runtime.
-             (let* ((out (assoc-ref outputs "out"))
+              ;; Make sure everything can run in a pure environment.
+              (let ((out (assoc-ref outputs "out"))
                     (path (getenv "PERL5LIB")))
-               (wrap-program (string-append out "/bin/edirect.pl")
-                 `("PERL5LIB" ":" prefix (,path))))
-             #t))
+                (for-each
+                  (lambda (file)
+                    (wrap-program file
+                      `("PERL5LIB" ":" prefix (,path)))
+                    (wrap-program file
+                      `("PATH" ":" prefix (,(string-append out "/bin")
+                                           ,(dirname (which "sed"))
+                                           ,(dirname (which "gzip"))
+                                           ,(dirname (which "grep"))
+                                           ,(dirname (which "perl"))
+                                           ,(dirname (which "uname"))))))
+                  (find-files out ".")))
+              #t))
          (add-after 'wrap-program 'check
            (lambda* (#:key outputs #:allow-other-keys)
              (invoke (string-append (assoc-ref outputs "out")
@@ -2801,7 +2830,8 @@ quantitative phenotypes.")
                      "-filter" "-help")
              #t)))))
     (inputs
-     `(("perl-html-parser" ,perl-html-parser)
+     `(("edirect-go-programs" ,edirect-go-programs)
+       ("perl-html-parser" ,perl-html-parser)
        ("perl-encode-locale" ,perl-encode-locale)
        ("perl-file-listing" ,perl-file-listing)
        ("perl-html-tagset" ,perl-html-tagset)
@@ -2831,6 +2861,13 @@ EDirect also provides an argument-driven function that simplifies the
 extraction of data from document summaries or other results that are returned
 in structured XML format.  This can eliminate the need for writing custom
 software to answer ad hoc questions.")
+    (native-search-paths
+     ;; Ideally this should be set for LWP somewhere.
+     (list (search-path-specification
+            (variable "PERL_LWP_SSL_CA_FILE")
+            (file-type 'regular)
+            (separator #f)
+            (files '("/etc/ssl/certs/ca-certificates.crt")))))
     (license license:public-domain)))
 
 (define-public edirect-go-programs
-- 
2.25.1

bug#40086: [PATCH 00/11] Expand edirect programs

[Efraim Flashner]

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Patches pushed


-- 
Efraim Flashner   <efraim@flashner.co.il>   אפרים פלשנר
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