1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
| | ;;; GNU Guix --- Functional package management for GNU
;;; Copyright © 2021 Ricardo Wurmus <rekado@elephly.net>
;;;
;;; This file is part of GNU Guix.
;;;
;;; GNU Guix is free software; you can redistribute it and/or modify it
;;; under the terms of the GNU General Public License as published by
;;; the Free Software Foundation; either version 3 of the License, or (at
;;; your option) any later version.
;;;
;;; GNU Guix is distributed in the hope that it will be useful, but
;;; WITHOUT ANY WARRANTY; without even the implied warranty of
;;; MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
;;; GNU General Public License for more details.
;;;
;;; You should have received a copy of the GNU General Public License
;;; along with GNU Guix. If not, see <http://www.gnu.org/licenses/>.
(define-module (gnu packages irods)
#:use-module ((guix licenses) #:prefix license:)
#:use-module (guix packages)
#:use-module (guix download)
#:use-module (guix build-system cmake)
#:use-module (guix utils)
#:use-module (gnu packages)
#:use-module (gnu packages backup)
#:use-module (gnu packages boost)
#:use-module (gnu packages check)
#:use-module (gnu packages compression)
#:use-module (gnu packages cpp)
#:use-module (gnu packages databases)
#:use-module (gnu packages gcc)
#:use-module (gnu packages kerberos)
#:use-module (gnu packages linux)
#:use-module (gnu packages llvm)
#:use-module (gnu packages logging)
#:use-module (gnu packages networking)
#:use-module (gnu packages pretty-print)
#:use-module (gnu packages python)
#:use-module (gnu packages serialization)
#:use-module (gnu packages tls)
#:use-module (srfi srfi-1))
(define-public irods
(package
(name "irods")
(version "4.2.8")
(source (origin
(method url-fetch)
(uri (string-append "https://github.com/irods/irods/releases/download/"
version "/irods-" version ".tar.gz"))
(sha256
(base32
"0ny54c3r0j692rvbr4iibg7xgd2i7g9x8yyrw04j889bywix14rc"))))
(build-system cmake-build-system)
(arguments
`(#:configure-flags
(list
"-DCMAKE_BUILD_TYPE=Release"
(string-append "-DCMAKE_MODULE_LINKER_FLAGS=-Wl,-rpath="
(assoc-ref %outputs "out") "/lib")
(string-append "-DCMAKE_SHARED_LINKER_FLAGS=-Wl,-rpath="
(assoc-ref %outputs "out") "/lib")
(string-append "-DCMAKE_EXE_LINKER_FLAGS=-Wl,-rpath="
(assoc-ref %outputs "out") "/lib")
;; Configuration aborts if no generator format is set
"-DCPACK_GENERATOR=TGZ"
;; Configuration attempts to guess the distribution with Python.
"-DIRODS_LINUX_DISTRIBUTION_NAME=guix"
"-DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR=1"
(string-append "-DIRODS_EXTERNALS_FULLPATH_CLANG="
(assoc-ref %build-inputs "clang"))
(string-append "-DIRODS_EXTERNALS_FULLPATH_CLANG_RUNTIME="
(assoc-ref %build-inputs "clang-runtime"))
(string-append "-DIRODS_EXTERNALS_FULLPATH_CPPZMQ="
(assoc-ref %build-inputs "cppzmq"))
(string-append "-DIRODS_EXTERNALS_FULLPATH_ARCHIVE="
(assoc-ref %build-inputs "libarchive"))
(string-append "-DIRODS_EXTERNALS_FULLPATH_AVRO="
(assoc-ref %build-inputs "avro-cpp"))
(string-append "-DIRODS_EXTERNALS_FULLPATH_BOOST="
(assoc-ref %build-inputs "boost"))
(string-append "-DIRODS_EXTERNALS_FULLPATH_ZMQ="
(assoc-ref %build-inputs "zeromq"))
(string-append "-DIRODS_EXTERNALS_FULLPATH_JSON="
(assoc-ref %build-inputs "json"))
(string-append "-DIRODS_EXTERNALS_FULLPATH_CATCH2="
(assoc-ref %build-inputs "catch2"))
(string-append "-DIRODS_EXTERNALS_FULLPATH_NANODBC="
(assoc-ref %build-inputs "nanodbc"))
(string-append "-DIRODS_EXTERNALS_FULLPATH_FMT="
(assoc-ref %build-inputs "fmt")))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'unset-Werror
(lambda _
;; -Werror kills the build due to a comparison REQUIRE(errs.size() == err->len);
;; in unit_tests/src/test_irods_lifetime_manager.cpp
(substitute* "CMakeLists.txt"
(("-Werror") ""))))
(add-after 'unpack 'remove-FHS-and-prefix-assumptions
(lambda* (#:key inputs #:allow-other-keys)
(substitute* '("CMakeLists.txt"
"cmake/server.cmake"
"cmake/development_library.cmake"
"cmake/runtime_library.cmake")
(("usr/") ""))
(substitute* "lib/core/src/irods_default_paths.cpp"
(("path.append\\(\"usr\"\\)") "path")
(("path.remove_filename\\(\\).remove_filename\\(\\).remove_filename\\(\\)")
"path.remove_filename().remove_filename()"))
(substitute* "scripts/irods/paths.py"
(("'usr', 'lib', 'irods'") "'lib', 'irods'"))
(substitute* "scripts/irods/pypyodbc.py"
(("\"/usr/lib/libodbc.so\"")
(string-append (assoc-ref inputs "unixodbc") "/lib/libodbc.so")))))
(add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
(lambda* (#:key inputs #:allow-other-keys)
(let ((gcc (assoc-ref inputs "gcc")))
(setenv "CPLUS_INCLUDE_PATH"
(string-join
(cons* (string-append (assoc-ref inputs "libcxx+libcxxabi")
"/include/c++/v1")
(string-append (assoc-ref inputs "catch2")
"/include/catch2")
(string-append (assoc-ref inputs "json")
"/include/nlohmann")
;; Hide GCC's C++ headers so that they do not interfere with
;; the Clang headers.
(delete (string-append gcc "/include/c++")
(string-split (getenv "CPLUS_INCLUDE_PATH")
#\:)))
":"))
(format #true
"environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
(getenv "CPLUS_INCLUDE_PATH"))))))))
(inputs
`(("avro-cpp" ,(package
(inherit avro-cpp-1.9)
(arguments
`(#:configure-flags
'("-DCMAKE_CXX_COMPILER=clang++"
"-DCMAKE_CXX_FLAGS=-stdlib=libc++"
"-DCMAKE_EXE_LINKER_FLAGS=-lc++abi -lz")
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'chdir
(lambda _ (chdir "lang/c++")))
(add-after 'set-paths 'adjust-CPLUS_INCLUDE_PATH
(lambda* (#:key inputs #:allow-other-keys)
(let ((gcc (assoc-ref inputs "gcc")))
(setenv "CPLUS_INCLUDE_PATH"
(string-join
(cons* (string-append (assoc-ref inputs "libcxx+libcxxabi")
"/include/c++/v1")
;; Hide GCC's C++ headers so that they do not interfere with
;; the Clang headers.
(delete (string-append gcc "/include/c++")
(string-split (getenv "CPLUS_INCLUDE_PATH")
#\:)))
":"))
(format #true
"environment variable `CPLUS_INCLUDE_PATH' changed to ~a~%"
(getenv "CPLUS_INCLUDE_PATH"))))))))
(inputs
`(("boost" ,boost-for-irods)
("clang" ,clang-toolchain-6)
("libcxx+libcxxabi" ,libcxx+libcxxabi-6)
("libcxxabi" ,libcxxabi-6)
("snappy" ,snappy-with-clang6)
("zlib" ,zlib)))))
("boost" ,boost-for-irods)
("cppzmq" ,cppzmq)
("fmt" ,fmt-for-irods)
("json" ,json-modern-cxx)
("libarchive" ,libarchive)
("libcxxabi" ,libcxxabi-6) ; we need this for linking with -lc++abi
("linux-pam" ,linux-pam)
("mit-krb5" ,mit-krb5)
("nanodbc" ,nanodbc-for-irods)
("openssl" ,openssl)
("python" ,python-wrapper)
("unixodbc" ,unixodbc)
("zeromq" ,zeromq)))
(native-inputs
`(("catch2" ,catch-framework2)
("clang" ,clang-toolchain-6)
("clang-runtime" ,clang-runtime-6)
("libcxx+libcxxabi" ,libcxx+libcxxabi-6)))
(home-page "https://irods.org")
(synopsis "Data management software")
(description "The Integrated Rule-Oriented Data System (iRODS) is data
management software. iRODS virtualizes data storage resources, so users can
take control of their data, regardless of where and on what device the data is
stored.")
(license license:bsd-3)))
|