comparison smart_toolShed/SMART/Java/LICENSE.txt @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.
author yufei-luo
date Thu, 17 Jan 2013 10:52:14 -0500
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1
2 CeCILL FREE SOFTWARE LICENSE AGREEMENT
3
4
5 Notice
6
7 This Agreement is a Free Software license agreement that is the result
8 of discussions between its authors in order to ensure compliance with
9 the two main principles guiding its drafting:
10
11 * firstly, compliance with the principles governing the distribution
12 of Free Software: access to source code, broad rights granted to
13 users,
14 * secondly, the election of a governing law, French law, with which
15 it is conformant, both as regards the law of torts and
16 intellectual property law, and the protection that it offers to
17 both authors and holders of the economic rights over software.
18
19 The authors of the CeCILL (for Ce[a] C[nrs] I[nria] L[ogiciel] L[ibre])
20 license are:
21
22 Commissariat à l'Energie Atomique - CEA, a public scientific, technical
23 and industrial research establishment, having its principal place of
24 business at 25 rue Leblanc, immeuble Le Ponant D, 75015 Paris, France.
25
26 Centre National de la Recherche Scientifique - CNRS, a public scientific
27 and technological establishment, having its principal place of business
28 at 3 rue Michel-Ange, 75794 Paris cedex 16, France.
29
30 Institut National de Recherche en Informatique et en Automatique -
31 INRIA, a public scientific and technological establishment, having its
32 principal place of business at Domaine de Voluceau, Rocquencourt, BP
33 105, 78153 Le Chesnay cedex, France.
34
35
36 Preamble
37
38 The purpose of this Free Software license agreement is to grant users
39 the right to modify and redistribute the software governed by this
40 license within the framework of an open source distribution model.
41
42 The exercising of these rights is conditional upon certain obligations
43 for users so as to preserve this status for all subsequent redistributions.
44
45 In consideration of access to the source code and the rights to copy,
46 modify and redistribute granted by the license, users are provided only
47 with a limited warranty and the software's author, the holder of the
48 economic rights, and the successive licensors only have limited liability.
49
50 In this respect, the risks associated with loading, using, modifying
51 and/or developing or reproducing the software by the user are brought to
52 the user's attention, given its Free Software status, which may make it
53 complicated to use, with the result that its use is reserved for
54 developers and experienced professionals having in-depth computer
55 knowledge. Users are therefore encouraged to load and test the
56 suitability of the software as regards their requirements in conditions
57 enabling the security of their systems and/or data to be ensured and,
58 more generally, to use and operate it in the same conditions of
59 security. This Agreement may be freely reproduced and published,
60 provided it is not altered, and that no provisions are either added or
61 removed herefrom.
62
63 This Agreement may apply to any or all software for which the holder of
64 the economic rights decides to submit the use thereof to its provisions.
65
66
67 Article 1 - DEFINITIONS
68
69 For the purpose of this Agreement, when the following expressions
70 commence with a capital letter, they shall have the following meaning:
71
72 Agreement: means this license agreement, and its possible subsequent
73 versions and annexes.
74
75 Software: means the software in its Object Code and/or Source Code form
76 and, where applicable, its documentation, "as is" when the Licensee
77 accepts the Agreement.
78
79 Initial Software: means the Software in its Source Code and possibly its
80 Object Code form and, where applicable, its documentation, "as is" when
81 it is first distributed under the terms and conditions of the Agreement.
82
83 Modified Software: means the Software modified by at least one
84 Contribution.
85
86 Source Code: means all the Software's instructions and program lines to
87 which access is required so as to modify the Software.
88
89 Object Code: means the binary files originating from the compilation of
90 the Source Code.
91
92 Holder: means the holder(s) of the economic rights over the Initial
93 Software.
94
95 Licensee: means the Software user(s) having accepted the Agreement.
96
97 Contributor: means a Licensee having made at least one Contribution.
98
99 Licensor: means the Holder, or any other individual or legal entity, who
100 distributes the Software under the Agreement.
101
102 Contribution: means any or all modifications, corrections, translations,
103 adaptations and/or new functions integrated into the Software by any or
104 all Contributors, as well as any or all Internal Modules.
105
106 Module: means a set of sources files including their documentation that
107 enables supplementary functions or services in addition to those offered
108 by the Software.
109
110 External Module: means any or all Modules, not derived from the
111 Software, so that this Module and the Software run in separate address
112 spaces, with one calling the other when they are run.
113
114 Internal Module: means any or all Module, connected to the Software so
115 that they both execute in the same address space.
116
117 GNU GPL: means the GNU General Public License version 2 or any
118 subsequent version, as published by the Free Software Foundation Inc.
119
120 Parties: mean both the Licensee and the Licensor.
121
122 These expressions may be used both in singular and plural form.
123
124
125 Article 2 - PURPOSE
126
127 The purpose of the Agreement is the grant by the Licensor to the
128 Licensee of a non-exclusive, transferable and worldwide license for the
129 Software as set forth in Article 5 hereinafter for the whole term of the
130 protection granted by the rights over said Software.
131
132
133 Article 3 - ACCEPTANCE
134
135 3.1 The Licensee shall be deemed as having accepted the terms and
136 conditions of this Agreement upon the occurrence of the first of the
137 following events:
138
139 * (i) loading the Software by any or all means, notably, by
140 downloading from a remote server, or by loading from a physical
141 medium;
142 * (ii) the first time the Licensee exercises any of the rights
143 granted hereunder.
144
145 3.2 One copy of the Agreement, containing a notice relating to the
146 characteristics of the Software, to the limited warranty, and to the
147 fact that its use is restricted to experienced users has been provided
148 to the Licensee prior to its acceptance as set forth in Article 3.1
149 hereinabove, and the Licensee hereby acknowledges that it has read and
150 understood it.
151
152
153 Article 4 - EFFECTIVE DATE AND TERM
154
155
156 4.1 EFFECTIVE DATE
157
158 The Agreement shall become effective on the date when it is accepted by
159 the Licensee as set forth in Article 3.1.
160
161
162 4.2 TERM
163
164 The Agreement shall remain in force for the entire legal term of
165 protection of the economic rights over the Software.
166
167
168 Article 5 - SCOPE OF RIGHTS GRANTED
169
170 The Licensor hereby grants to the Licensee, who accepts, the following
171 rights over the Software for any or all use, and for the term of the
172 Agreement, on the basis of the terms and conditions set forth hereinafter.
173
174 Besides, if the Licensor owns or comes to own one or more patents
175 protecting all or part of the functions of the Software or of its
176 components, the Licensor undertakes not to enforce the rights granted by
177 these patents against successive Licensees using, exploiting or
178 modifying the Software. If these patents are transferred, the Licensor
179 undertakes to have the transferees subscribe to the obligations set
180 forth in this paragraph.
181
182
183 5.1 RIGHT OF USE
184
185 The Licensee is authorized to use the Software, without any limitation
186 as to its fields of application, with it being hereinafter specified
187 that this comprises:
188
189 1. permanent or temporary reproduction of all or part of the Software
190 by any or all means and in any or all form.
191
192 2. loading, displaying, running, or storing the Software on any or
193 all medium.
194
195 3. entitlement to observe, study or test its operation so as to
196 determine the ideas and principles behind any or all constituent
197 elements of said Software. This shall apply when the Licensee
198 carries out any or all loading, displaying, running, transmission
199 or storage operation as regards the Software, that it is entitled
200 to carry out hereunder.
201
202
203 5.2 ENTITLEMENT TO MAKE CONTRIBUTIONS
204
205 The right to make Contributions includes the right to translate, adapt,
206 arrange, or make any or all modifications to the Software, and the right
207 to reproduce the resulting software.
208
209 The Licensee is authorized to make any or all Contributions to the
210 Software provided that it includes an explicit notice that it is the
211 author of said Contribution and indicates the date of the creation thereof.
212
213
214 5.3 RIGHT OF DISTRIBUTION
215
216 In particular, the right of distribution includes the right to publish,
217 transmit and communicate the Software to the general public on any or
218 all medium, and by any or all means, and the right to market, either in
219 consideration of a fee, or free of charge, one or more copies of the
220 Software by any means.
221
222 The Licensee is further authorized to distribute copies of the modified
223 or unmodified Software to third parties according to the terms and
224 conditions set forth hereinafter.
225
226
227 5.3.1 DISTRIBUTION OF SOFTWARE WITHOUT MODIFICATION
228
229 The Licensee is authorized to distribute true copies of the Software in
230 Source Code or Object Code form, provided that said distribution
231 complies with all the provisions of the Agreement and is accompanied by:
232
233 1. a copy of the Agreement,
234
235 2. a notice relating to the limitation of both the Licensor's
236 warranty and liability as set forth in Articles 8 and 9,
237
238 and that, in the event that only the Object Code of the Software is
239 redistributed, the Licensee allows future Licensees unhindered access to
240 the full Source Code of the Software by indicating how to access it, it
241 being understood that the additional cost of acquiring the Source Code
242 shall not exceed the cost of transferring the data.
243
244
245 5.3.2 DISTRIBUTION OF MODIFIED SOFTWARE
246
247 When the Licensee makes a Contribution to the Software, the terms and
248 conditions for the distribution of the resulting Modified Software
249 become subject to all the provisions of this Agreement.
250
251 The Licensee is authorized to distribute the Modified Software, in
252 source code or object code form, provided that said distribution
253 complies with all the provisions of the Agreement and is accompanied by:
254
255 1. a copy of the Agreement,
256
257 2. a notice relating to the limitation of both the Licensor's
258 warranty and liability as set forth in Articles 8 and 9,
259
260 and that, in the event that only the object code of the Modified
261 Software is redistributed, the Licensee allows future Licensees
262 unhindered access to the full source code of the Modified Software by
263 indicating how to access it, it being understood that the additional
264 cost of acquiring the source code shall not exceed the cost of
265 transferring the data.
266
267
268 5.3.3 DISTRIBUTION OF EXTERNAL MODULES
269
270 When the Licensee has developed an External Module, the terms and
271 conditions of this Agreement do not apply to said External Module, that
272 may be distributed under a separate license agreement.
273
274
275 5.3.4 COMPATIBILITY WITH THE GNU GPL
276
277 The Licensee can include a code that is subject to the provisions of one
278 of the versions of the GNU GPL in the Modified or unmodified Software,
279 and distribute that entire code under the terms of the same version of
280 the GNU GPL.
281
282 The Licensee can include the Modified or unmodified Software in a code
283 that is subject to the provisions of one of the versions of the GNU GPL,
284 and distribute that entire code under the terms of the same version of
285 the GNU GPL.
286
287
288 Article 6 - INTELLECTUAL PROPERTY
289
290
291 6.1 OVER THE INITIAL SOFTWARE
292
293 The Holder owns the economic rights over the Initial Software. Any or
294 all use of the Initial Software is subject to compliance with the terms
295 and conditions under which the Holder has elected to distribute its work
296 and no one shall be entitled to modify the terms and conditions for the
297 distribution of said Initial Software.
298
299 The Holder undertakes that the Initial Software will remain ruled at
300 least by this Agreement, for the duration set forth in Article 4.2.
301
302
303 6.2 OVER THE CONTRIBUTIONS
304
305 The Licensee who develops a Contribution is the owner of the
306 intellectual property rights over this Contribution as defined by
307 applicable law.
308
309
310 6.3 OVER THE EXTERNAL MODULES
311
312 The Licensee who develops an External Module is the owner of the
313 intellectual property rights over this External Module as defined by
314 applicable law and is free to choose the type of agreement that shall
315 govern its distribution.
316
317
318 6.4 JOINT PROVISIONS
319
320 The Licensee expressly undertakes:
321
322 1. not to remove, or modify, in any manner, the intellectual property
323 notices attached to the Software;
324
325 2. to reproduce said notices, in an identical manner, in the copies
326 of the Software modified or not.
327
328 The Licensee undertakes not to directly or indirectly infringe the
329 intellectual property rights of the Holder and/or Contributors on the
330 Software and to take, where applicable, vis-à-vis its staff, any and all
331 measures required to ensure respect of said intellectual property rights
332 of the Holder and/or Contributors.
333
334
335 Article 7 - RELATED SERVICES
336
337 7.1 Under no circumstances shall the Agreement oblige the Licensor to
338 provide technical assistance or maintenance services for the Software.
339
340 However, the Licensor is entitled to offer this type of services. The
341 terms and conditions of such technical assistance, and/or such
342 maintenance, shall be set forth in a separate instrument. Only the
343 Licensor offering said maintenance and/or technical assistance services
344 shall incur liability therefor.
345
346 7.2 Similarly, any Licensor is entitled to offer to its licensees, under
347 its sole responsibility, a warranty, that shall only be binding upon
348 itself, for the redistribution of the Software and/or the Modified
349 Software, under terms and conditions that it is free to decide. Said
350 warranty, and the financial terms and conditions of its application,
351 shall be subject of a separate instrument executed between the Licensor
352 and the Licensee.
353
354
355 Article 8 - LIABILITY
356
357 8.1 Subject to the provisions of Article 8.2, the Licensee shall be
358 entitled to claim compensation for any direct loss it may have suffered
359 from the Software as a result of a fault on the part of the relevant
360 Licensor, subject to providing evidence thereof.
361
362 8.2 The Licensor's liability is limited to the commitments made under
363 this Agreement and shall not be incurred as a result of in particular:
364 (i) loss due the Licensee's total or partial failure to fulfill its
365 obligations, (ii) direct or consequential loss that is suffered by the
366 Licensee due to the use or performance of the Software, and (iii) more
367 generally, any consequential loss. In particular the Parties expressly
368 agree that any or all pecuniary or business loss (i.e. loss of data,
369 loss of profits, operating loss, loss of customers or orders,
370 opportunity cost, any disturbance to business activities) or any or all
371 legal proceedings instituted against the Licensee by a third party,
372 shall constitute consequential loss and shall not provide entitlement to
373 any or all compensation from the Licensor.
374
375
376 Article 9 - WARRANTY
377
378 9.1 The Licensee acknowledges that the scientific and technical
379 state-of-the-art when the Software was distributed did not enable all
380 possible uses to be tested and verified, nor for the presence of
381 possible defects to be detected. In this respect, the Licensee's
382 attention has been drawn to the risks associated with loading, using,
383 modifying and/or developing and reproducing the Software which are
384 reserved for experienced users.
385
386 The Licensee shall be responsible for verifying, by any or all means,
387 the suitability of the product for its requirements, its good working
388 order, and for ensuring that it shall not cause damage to either persons
389 or properties.
390
391 9.2 The Licensor hereby represents, in good faith, that it is entitled
392 to grant all the rights over the Software (including in particular the
393 rights set forth in Article 5).
394
395 9.3 The Licensee acknowledges that the Software is supplied "as is" by
396 the Licensor without any other express or tacit warranty, other than
397 that provided for in Article 9.2 and, in particular, without any warranty
398 as to its commercial value, its secured, safe, innovative or relevant
399 nature.
400
401 Specifically, the Licensor does not warrant that the Software is free
402 from any error, that it will operate without interruption, that it will
403 be compatible with the Licensee's own equipment and software
404 configuration, nor that it will meet the Licensee's requirements.
405
406 9.4 The Licensor does not either expressly or tacitly warrant that the
407 Software does not infringe any third party intellectual property right
408 relating to a patent, software or any other property right. Therefore,
409 the Licensor disclaims any and all liability towards the Licensee
410 arising out of any or all proceedings for infringement that may be
411 instituted in respect of the use, modification and redistribution of the
412 Software. Nevertheless, should such proceedings be instituted against
413 the Licensee, the Licensor shall provide it with technical and legal
414 assistance for its defense. Such technical and legal assistance shall be
415 decided on a case-by-case basis between the relevant Licensor and the
416 Licensee pursuant to a memorandum of understanding. The Licensor
417 disclaims any and all liability as regards the Licensee's use of the
418 name of the Software. No warranty is given as regards the existence of
419 prior rights over the name of the Software or as regards the existence
420 of a trademark.
421
422
423 Article 10 - TERMINATION
424
425 10.1 In the event of a breach by the Licensee of its obligations
426 hereunder, the Licensor may automatically terminate this Agreement
427 thirty (30) days after notice has been sent to the Licensee and has
428 remained ineffective.
429
430 10.2 A Licensee whose Agreement is terminated shall no longer be
431 authorized to use, modify or distribute the Software. However, any
432 licenses that it may have granted prior to termination of the Agreement
433 shall remain valid subject to their having been granted in compliance
434 with the terms and conditions hereof.
435
436
437 Article 11 - MISCELLANEOUS
438
439
440 11.1 EXCUSABLE EVENTS
441
442 Neither Party shall be liable for any or all delay, or failure to
443 perform the Agreement, that may be attributable to an event of force
444 majeure, an act of God or an outside cause, such as defective
445 functioning or interruptions of the electricity or telecommunications
446 networks, network paralysis following a virus attack, intervention by
447 government authorities, natural disasters, water damage, earthquakes,
448 fire, explosions, strikes and labor unrest, war, etc.
449
450 11.2 Any failure by either Party, on one or more occasions, to invoke
451 one or more of the provisions hereof, shall under no circumstances be
452 interpreted as being a waiver by the interested Party of its right to
453 invoke said provision(s) subsequently.
454
455 11.3 The Agreement cancels and replaces any or all previous agreements,
456 whether written or oral, between the Parties and having the same
457 purpose, and constitutes the entirety of the agreement between said
458 Parties concerning said purpose. No supplement or modification to the
459 terms and conditions hereof shall be effective as between the Parties
460 unless it is made in writing and signed by their duly authorized
461 representatives.
462
463 11.4 In the event that one or more of the provisions hereof were to
464 conflict with a current or future applicable act or legislative text,
465 said act or legislative text shall prevail, and the Parties shall make
466 the necessary amendments so as to comply with said act or legislative
467 text. All other provisions shall remain effective. Similarly, invalidity
468 of a provision of the Agreement, for any reason whatsoever, shall not
469 cause the Agreement as a whole to be invalid.
470
471
472 11.5 LANGUAGE
473
474 The Agreement is drafted in both French and English and both versions
475 are deemed authentic.
476
477
478 Article 12 - NEW VERSIONS OF THE AGREEMENT
479
480 12.1 Any person is authorized to duplicate and distribute copies of this
481 Agreement.
482
483 12.2 So as to ensure coherence, the wording of this Agreement is
484 protected and may only be modified by the authors of the License, who
485 reserve the right to periodically publish updates or new versions of the
486 Agreement, each with a separate number. These subsequent versions may
487 address new issues encountered by Free Software.
488
489 12.3 Any Software distributed under a given version of the Agreement may
490 only be subsequently distributed under the same version of the Agreement
491 or a subsequent version, subject to the provisions of Article 5.3.4.
492
493
494 Article 13 - GOVERNING LAW AND JURISDICTION
495
496 13.1 The Agreement is governed by French law. The Parties agree to
497 endeavor to seek an amicable solution to any disagreements or disputes
498 that may arise during the performance of the Agreement.
499
500 13.2 Failing an amicable solution within two (2) months as from their
501 occurrence, and unless emergency proceedings are necessary, the
502 disagreements or disputes shall be referred to the Paris Courts having
503 jurisdiction, by the more diligent Party.
504
505
506 Version 2.0 dated 2006-09-05.