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
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
|
;;; 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 git-download)
#:use-module (guix build-system cmake)
#:use-module (guix utils)
#:use-module (gnu packages)
#:use-module (gnu packages backup)
#:use-module (gnu packages base)
#: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 man)
#: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\"")
(search-input-file inputs "/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* (search-input-directory inputs "/include/c++/v1")
(search-input-directory inputs "/include/catch2")
(search-input-directory inputs "/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" ,avro-cpp-1.9-for-irods)
("boost" ,boost-for-irods)
("cppzmq" ,cppzmq)
("fmt" ,fmt-6)
("json" ,nlohmann-json)
("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" ,catch2)
("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)))
(define-public irods-client-icommands
(package
(name "irods-client-icommands")
(version "4.2.8")
(source (origin
(method git-fetch)
(uri (git-reference
(url "https://github.com/irods/irods_client_icommands")
(commit version)))
(file-name (git-file-name name version))
(sha256
(base32
"069n647p5ypf44gim8z26mwayg5lzgk7r9qyyqd8f9n7h0p4jxpn"))))
(build-system cmake-build-system)
(arguments
`(#:tests? #false ; not clear how to run tests
#:configure-flags
(list
"-DCMAKE_BUILD_TYPE=Release"
;; Configuration attempts to guess the distribution with Python.
"-DIRODS_LINUX_DISTRIBUTION_NAME=guix"
"-DIRODS_LINUX_DISTRIBUTION_VERSION_MAJOR=1"
(string-append "-DIRODS_DIR="
(assoc-ref %build-inputs "irods")
"/lib/irods/cmake")
(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_FMT="
(assoc-ref %build-inputs "fmt")))
#:phases
(modify-phases %standard-phases
(add-after 'unpack 'unset-Werror ;
(lambda _ ;
;; -Werror kills the build due to a deprecation warning
(substitute* "CMakeLists.txt" ;
(("-Werror") ""))))
(add-after 'unpack 'remove-/usr-prefix
(lambda _
(substitute* "CMakeLists.txt"
(("usr/") ""))))
(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* (search-input-directory inputs
"include/c++/v1")
(search-input-directory inputs
"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" ,avro-cpp-1.9-for-irods)
("boost" ,boost-for-irods)
("cppzmq" ,cppzmq)
("fmt" ,fmt-6)
("irods" ,irods)
("json" ,nlohmann-json)
("libarchive" ,libarchive)
("libcxxabi" ,libcxxabi-6) ; we need this for linking with -lc++abi
("mit-krb5" ,mit-krb5)
("openssl" ,openssl)
("zeromq" ,zeromq)))
(native-inputs
`(("clang" ,clang-toolchain-6)
("clang-runtime" ,clang-runtime-6)
("libcxx+libcxxabi" ,libcxx+libcxxabi-6)
("help2man" ,help2man)
("which" ,which)))
(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)))
|