From 303aa3021d9f19851f847ace120acafb1701d747 Mon Sep 17 00:00:00 2001 From: edgano Date: Wed, 17 Apr 2019 14:14:11 +0200 Subject: [PATCH 1/7] 1st amap --- recipes/amap/build.sh | 16 ++++++++++++++++ recipes/amap/meta.yaml | 34 ++++++++++++++++++++++++++++++++++ recipes/amap/patch.file | 13 +++++++++++++ 3 files changed, 63 insertions(+) create mode 100644 recipes/amap/build.sh create mode 100644 recipes/amap/meta.yaml create mode 100644 recipes/amap/patch.file diff --git a/recipes/amap/build.sh b/recipes/amap/build.sh new file mode 100644 index 0000000000000..a6cf6ba0d2dc1 --- /dev/null +++ b/recipes/amap/build.sh @@ -0,0 +1,16 @@ +#!/bin/bash +# +# CONDA build script variables +# +# $PREFIX The install prefix +# $PKG_NAME The name of the package +# $PKG_VERSION The version of the package +# $PKG_BUILDNUM The build number of the package +# +set -eu -o pipefail + +cd align +make + +mkdir -p $PREFIX/bin +cp amap $PREFIX/bin diff --git a/recipes/amap/meta.yaml b/recipes/amap/meta.yaml new file mode 100644 index 0000000000000..0000bc7f4482f --- /dev/null +++ b/recipes/amap/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "2.2" %} + +package: + name: amap + version: {{ version }} + +build: + number: 0 + +source: + url: https://github.com/mes5k/amap-align/archive/600fc29fb9d0e8a6abf797c173c7a416ab99c541.zip + sha256: 57391561dfa0ec0e291a11f54177cfcf17baa47be065f0cc688e4bb98de792b4 + patches: + - patch.file + +requirements: + build: + - {{ compiler('cxx') }} + + run: + - blast + +test: + commands: + - amap -gui + +about: + home: "https://web.archive.org/web/20060902044446/http://bio.math.berkeley.edu/amap/" + license: "GPL" + summary: "AMAP is a multiple sequence alignment program based on sequence annealing." + +extra: + identifiers: + - doi:10.1093/bioinformatics/btl311 \ No newline at end of file diff --git a/recipes/amap/patch.file b/recipes/amap/patch.file new file mode 100644 index 0000000000000..1fc6fb1a9041f --- /dev/null +++ b/recipes/amap/patch.file @@ -0,0 +1,13 @@ +diff --git a/align/Amap.cc b/align/Amap.cc +index bb631b0..5949f7b 100644 +--- a/align/Amap.cc ++++ b/align/Amap.cc +@@ -23,6 +23,8 @@ + #include + #include + #include ++#include //BUG strcmp ++#include + + string parametersInputFilename = ""; + string parametersOutputFilename = "no training"; From ba27243beaeb31872a5919328f03a386e35dd427 Mon Sep 17 00:00:00 2001 From: Edgar Garriga Date: Wed, 17 Apr 2019 23:36:44 +0200 Subject: [PATCH 2/7] fix patch --- recipes/amap/patch.file | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/recipes/amap/patch.file b/recipes/amap/patch.file index 1fc6fb1a9041f..edca1f3188228 100644 --- a/recipes/amap/patch.file +++ b/recipes/amap/patch.file @@ -1,7 +1,6 @@ -diff --git a/align/Amap.cc b/align/Amap.cc -index bb631b0..5949f7b 100644 ---- a/align/Amap.cc -+++ b/align/Amap.cc +diff -ruN amap_raw/align/Amap.cc amap_new/align/Amap.cc +--- amap_raw/align/Amap.cc 2008-02-13 15:36:30.000000000 +0100 ++++ amap_new/align/Amap.cc 2019-04-17 23:32:47.000000000 +0200 @@ -23,6 +23,8 @@ #include #include @@ -11,3 +10,15 @@ index bb631b0..5949f7b 100644 string parametersInputFilename = ""; string parametersOutputFilename = "no training"; +diff -ruN amap_raw/align/Makefile amap_new/align/Makefile +--- amap_raw/align/Makefile 2008-02-13 15:36:30.000000000 +0100 ++++ amap_new/align/Makefile 2019-04-17 23:32:49.000000000 +0200 +@@ -6,7 +6,7 @@ + # 1) Choose C++ compiler. + ################################################################################ + +-CXX = g++ ++# CXX = g++ + + ################################################################################ + # 2) Set C++ flags. From d412b2d87b67fc4a5852012138ac0579449a3f2d Mon Sep 17 00:00:00 2001 From: Edgar Garriga Date: Thu, 18 Apr 2019 17:34:37 +0200 Subject: [PATCH 3/7] add GPL info --- recipes/amap/meta.yaml | 8 +++++--- 1 file changed, 5 insertions(+), 3 deletions(-) diff --git a/recipes/amap/meta.yaml b/recipes/amap/meta.yaml index 0000bc7f4482f..209cd6c277740 100644 --- a/recipes/amap/meta.yaml +++ b/recipes/amap/meta.yaml @@ -25,9 +25,11 @@ test: - amap -gui about: - home: "https://web.archive.org/web/20060902044446/http://bio.math.berkeley.edu/amap/" - license: "GPL" - summary: "AMAP is a multiple sequence alignment program based on sequence annealing." + home: https://web.archive.org/web/20060902044446/http://bio.math.berkeley.edu/amap/ + license: GPL-2 + license_file: /license/License.txt + summary: AMAP is a multiple sequence alignment program based on sequence annealing + dev_url: https://github.com/mes5k/amap-align extra: identifiers: From 3376ac9080464ce4424bfec17f19a45354fa4a12 Mon Sep 17 00:00:00 2001 From: Edgar Garriga Date: Thu, 18 Apr 2019 18:26:36 +0200 Subject: [PATCH 4/7] add license file --- recipes/amap/License.txt | 286 +++++++++++++++++++++++++++++++++++++++ recipes/amap/meta.yaml | 2 +- 2 files changed, 287 insertions(+), 1 deletion(-) create mode 100755 recipes/amap/License.txt diff --git a/recipes/amap/License.txt b/recipes/amap/License.txt new file mode 100755 index 0000000000000..ae17f53dfd710 --- /dev/null +++ b/recipes/amap/License.txt @@ -0,0 +1,286 @@ +The GNU General Public License (GPL) +Version 2, June 1991 + +Copyright (C) 1989, 1991 Free Software Foundation, Inc. + +59 Temple Place, Suite 330, Boston, MA 02111-1307 USA + +Everyone is permitted to copy and distribute verbatim copies + +of this license document, but changing it is not allowed. + + +Preamble + + +The licenses for most software are designed to take away your +freedom to share and change it. By contrast, the GNU General Public +License is intended to guarantee your freedom to share and change free +software--to make sure the software is free for all its users. This +General Public License applies to most of the Free Software +Foundation's software and to any other program whose authors commit to +using it. (Some other Free Software Foundation software is covered by +the GNU Library General Public License instead.) You can apply it to +your programs, too. + +When we speak of free software, we are referring to freedom, not +price. Our General Public Licenses are designed to make sure that you +have the freedom to distribute copies of free software (and charge for +this service if you wish), that you receive source code or can get it +if you want it, that you can change the software or use pieces of it +in new free programs; and that you know you can do these things. + +To protect your rights, we need to make restrictions that forbid +anyone to deny you these rights or to ask you to surrender the rights. +These restrictions translate to certain responsibilities for you if you +distribute copies of the software, or if you modify it. + +For example, if you distribute copies of such a program, whether +gratis or for a fee, you must give the recipients all the rights that +you have. You must make sure that they, too, receive or can get the +source code. And you must show them these terms so they know their +rights. + +We protect your rights with two steps: (1) copyright the software, and +(2) offer you this license which gives you legal permission to copy, +distribute and/or modify the software. + +Also, for each author's protection and ours, we want to make certain +that everyone understands that there is no warranty for this free +software. If the software is modified by someone else and passed on, we +want its recipients to know that what they have is not the original, so +that any problems introduced by others will not reflect on the original +authors' reputations. + +Finally, any free program is threatened constantly by software +patents. We wish to avoid the danger that redistributors of a free +program will individually obtain patent licenses, in effect making the +program proprietary. To prevent this, we have made it clear that any +patent must be licensed for everyone's free use or not licensed at all. + +The precise terms and conditions for copying, distribution and +modification follow. + + +TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION + + +0. This License applies to any program or other work which contains +a notice placed by the copyright holder saying it may be distributed +under the terms of this General Public License. The "Program", below, +refers to any such program or work, and a "work based on the Program" +means either the Program or any derivative work under copyright law: +that is to say, a work containing the Program or a portion of it, +either verbatim or with modifications and/or translated into another +language. (Hereinafter, translation is included without limitation in +the term "modification".) Each licensee is addressed as "you". + +Activities other than copying, distribution and modification are not +covered by this License; they are outside its scope. The act of +running the Program is not restricted, and the output from the Program +is covered only if its contents constitute a work based on the +Program (independent of having been made by running the Program). +Whether that is true depends on what the Program does. + +1. You may copy and distribute verbatim copies of the Program's +source code as you receive it, in any medium, provided that you +conspicuously and appropriately publish on each copy an appropriate +copyright notice and disclaimer of warranty; keep intact all the +notices that refer to this License and to the absence of any warranty; +and give any other recipients of the Program a copy of this License +along with the Program. + +You may charge a fee for the physical act of transferring a copy, and +you may at your option offer warranty protection in exchange for a fee. + +2. You may modify your copy or copies of the Program or any portion +of it, thus forming a work based on the Program, and copy and +distribute such modifications or work under the terms of Section 1 +above, provided that you also meet all of these conditions: + +a) You must cause the modified files to carry prominent notices +stating that you changed the files and the date of any change. + +b) You must cause any work that you distribute or publish, that in +whole or in part contains or is derived from the Program or any +part thereof, to be licensed as a whole at no charge to all third +parties under the terms of this License. + +c) If the modified program normally reads commands interactively +when run, you must cause it, when started running for such +interactive use in the most ordinary way, to print or display an +announcement including an appropriate copyright notice and a +notice that there is no warranty (or else, saying that you provide +a warranty) and that users may redistribute the program under +these conditions, and telling the user how to view a copy of this +License. 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But when you +distribute the same sections as part of a whole which is a work based +on the Program, the distribution of the whole must be on the terms of +this License, whose permissions for other licensees extend to the +entire whole, and thus to each and every part regardless of who wrote it. + +Thus, it is not the intent of this section to claim rights or contest +your rights to work written entirely by you; rather, the intent is to +exercise the right to control the distribution of derivative or +collective works based on the Program. + +In addition, mere aggregation of another work not based on the Program +with the Program (or with a work based on the Program) on a volume of +a storage or distribution medium does not bring the other work under +the scope of this License. + +3. You may copy and distribute the Program (or a work based on it, +under Section 2) in object code or executable form under the terms of +Sections 1 and 2 above provided that you also do one of the following: + +a) Accompany it with the complete corresponding machine-readable +source code, which must be distributed under the terms of Sections +1 and 2 above on a medium customarily used for software interchange; or, + +b) Accompany it with a written offer, valid for at least three +years, to give any third party, for a charge no more than your +cost of physically performing source distribution, a complete +machine-readable copy of the corresponding source code, to be +distributed under the terms of Sections 1 and 2 above on a medium +customarily used for software interchange; or, + +c) Accompany it with the information you received as to the offer +to distribute corresponding source code. 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Any attempt +otherwise to copy, modify, sublicense or distribute the Program is +void, and will automatically terminate your rights under this License. +However, parties who have received copies, or rights, from you under +this License will not have their licenses terminated so long as such +parties remain in full compliance. + +5. You are not required to accept this License, since you have not +signed it. However, nothing else grants you permission to modify or +distribute the Program or its derivative works. These actions are +prohibited by law if you do not accept this License. Therefore, by +modifying or distributing the Program (or any work based on the +Program), you indicate your acceptance of this License to do so, and +all its terms and conditions for copying, distributing or modifying +the Program or works based on it. + +6. Each time you redistribute the Program (or any work based on the +Program), the recipient automatically receives a license from the +original licensor to copy, distribute or modify the Program subject to +these terms and conditions. You may not impose any further +restrictions on the recipients' exercise of the rights granted herein. +You are not responsible for enforcing compliance by third parties to +this License. + +7. If, as a consequence of a court judgment or allegation of patent +infringement or for any other reason (not limited to patent issues), +conditions are imposed on you (whether by court order, agreement or +otherwise) that contradict the conditions of this License, they do not +excuse you from the conditions of this License. If you cannot +distribute so as to satisfy simultaneously your obligations under this +License and any other pertinent obligations, then as a consequence you +may not distribute the Program at all. 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The Free Software Foundation may publish revised and/or new versions +of the General Public License from time to time. Such new versions will +be similar in spirit to the present version, but may differ in detail to +address new problems or concerns. + +Each version is given a distinguishing version number. If the Program +specifies a version number of this License which applies to it and "any +later version", you have the option of following the terms and conditions +either of that version or of any later version published by the Free +Software Foundation. If the Program does not specify a version number of +this License, you may choose any version ever published by the Free Software +Foundation. + +10. If you wish to incorporate parts of the Program into other free +programs whose distribution conditions are different, write to the author +to ask for permission. For software which is copyrighted by the Free +Software Foundation, write to the Free Software Foundation; we sometimes +make exceptions for this. Our decision will be guided by the two goals +of preserving the free status of all derivatives of our free software and +of promoting the sharing and reuse of software generally. + +NO WARRANTY + +11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY +FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN +OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES +PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED +OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF +MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS +TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE +PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, +REPAIR OR CORRECTION. + +12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING +WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR +REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, +INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING +OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED +TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY +YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER +PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE +POSSIBILITY OF SUCH DAMAGES. + +END OF TERMS AND CONDITIONS diff --git a/recipes/amap/meta.yaml b/recipes/amap/meta.yaml index 209cd6c277740..b68795795311e 100644 --- a/recipes/amap/meta.yaml +++ b/recipes/amap/meta.yaml @@ -27,7 +27,7 @@ test: about: home: https://web.archive.org/web/20060902044446/http://bio.math.berkeley.edu/amap/ license: GPL-2 - license_file: /license/License.txt + license_file: License.txt summary: AMAP is a multiple sequence alignment program based on sequence annealing dev_url: https://github.com/mes5k/amap-align From 89bdf2000a07c95ef5da87bc123e65c5cf2b683d Mon Sep 17 00:00:00 2001 From: Edgar Garriga Date: Thu, 18 Apr 2019 19:00:04 +0200 Subject: [PATCH 5/7] retry for http error --- recipes/amap/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/amap/meta.yaml b/recipes/amap/meta.yaml index b68795795311e..8a6019a31804e 100644 --- a/recipes/amap/meta.yaml +++ b/recipes/amap/meta.yaml @@ -28,7 +28,7 @@ about: home: https://web.archive.org/web/20060902044446/http://bio.math.berkeley.edu/amap/ license: GPL-2 license_file: License.txt - summary: AMAP is a multiple sequence alignment program based on sequence annealing + summary: AMAP is a multiple sequence alignment program based on sequence annealing. dev_url: https://github.com/mes5k/amap-align extra: From d1decf8ce3bab6eb5af1aa14449eb3e0cde0b4a3 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Thu, 18 Apr 2019 22:18:24 +0200 Subject: [PATCH 6/7] Remove extra license file --- recipes/amap/License.txt | 286 --------------------------------------- 1 file changed, 286 deletions(-) delete mode 100755 recipes/amap/License.txt diff --git a/recipes/amap/License.txt b/recipes/amap/License.txt deleted file mode 100755 index ae17f53dfd710..0000000000000 --- a/recipes/amap/License.txt +++ /dev/null @@ -1,286 +0,0 @@ -The GNU General Public License (GPL) -Version 2, June 1991 - -Copyright (C) 1989, 1991 Free Software Foundation, Inc. - -59 Temple Place, Suite 330, Boston, MA 02111-1307 USA - -Everyone is permitted to copy and distribute verbatim copies - -of this license document, but changing it is not allowed. - - -Preamble - - -The licenses for most software are designed to take away your -freedom to share and change it. By contrast, the GNU General Public -License is intended to guarantee your freedom to share and change free -software--to make sure the software is free for all its users. This -General Public License applies to most of the Free Software -Foundation's software and to any other program whose authors commit to -using it. (Some other Free Software Foundation software is covered by -the GNU Library General Public License instead.) You can apply it to -your programs, too. - -When we speak of free software, we are referring to freedom, not -price. Our General Public Licenses are designed to make sure that you -have the freedom to distribute copies of free software (and charge for -this service if you wish), that you receive source code or can get it -if you want it, that you can change the software or use pieces of it -in new free programs; and that you know you can do these things. - -To protect your rights, we need to make restrictions that forbid -anyone to deny you these rights or to ask you to surrender the rights. -These restrictions translate to certain responsibilities for you if you -distribute copies of the software, or if you modify it. - -For example, if you distribute copies of such a program, whether -gratis or for a fee, you must give the recipients all the rights that -you have. You must make sure that they, too, receive or can get the -source code. And you must show them these terms so they know their -rights. - -We protect your rights with two steps: (1) copyright the software, and -(2) offer you this license which gives you legal permission to copy, -distribute and/or modify the software. - -Also, for each author's protection and ours, we want to make certain -that everyone understands that there is no warranty for this free -software. If the software is modified by someone else and passed on, we -want its recipients to know that what they have is not the original, so -that any problems introduced by others will not reflect on the original -authors' reputations. - -Finally, any free program is threatened constantly by software -patents. We wish to avoid the danger that redistributors of a free -program will individually obtain patent licenses, in effect making the -program proprietary. To prevent this, we have made it clear that any -patent must be licensed for everyone's free use or not licensed at all. - -The precise terms and conditions for copying, distribution and -modification follow. - - -TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION - - -0. This License applies to any program or other work which contains -a notice placed by the copyright holder saying it may be distributed -under the terms of this General Public License. The "Program", below, -refers to any such program or work, and a "work based on the Program" -means either the Program or any derivative work under copyright law: -that is to say, a work containing the Program or a portion of it, -either verbatim or with modifications and/or translated into another -language. (Hereinafter, translation is included without limitation in -the term "modification".) Each licensee is addressed as "you". - -Activities other than copying, distribution and modification are not -covered by this License; they are outside its scope. The act of -running the Program is not restricted, and the output from the Program -is covered only if its contents constitute a work based on the -Program (independent of having been made by running the Program). -Whether that is true depends on what the Program does. - -1. You may copy and distribute verbatim copies of the Program's -source code as you receive it, in any medium, provided that you -conspicuously and appropriately publish on each copy an appropriate -copyright notice and disclaimer of warranty; keep intact all the -notices that refer to this License and to the absence of any warranty; -and give any other recipients of the Program a copy of this License -along with the Program. - -You may charge a fee for the physical act of transferring a copy, and -you may at your option offer warranty protection in exchange for a fee. - -2. You may modify your copy or copies of the Program or any portion -of it, thus forming a work based on the Program, and copy and -distribute such modifications or work under the terms of Section 1 -above, provided that you also meet all of these conditions: - -a) You must cause the modified files to carry prominent notices -stating that you changed the files and the date of any change. - -b) You must cause any work that you distribute or publish, that in -whole or in part contains or is derived from the Program or any -part thereof, to be licensed as a whole at no charge to all third -parties under the terms of this License. - -c) If the modified program normally reads commands interactively -when run, you must cause it, when started running for such -interactive use in the most ordinary way, to print or display an -announcement including an appropriate copyright notice and a -notice that there is no warranty (or else, saying that you provide -a warranty) and that users may redistribute the program under -these conditions, and telling the user how to view a copy of this -License. (Exception: if the Program itself is interactive but -does not normally print such an announcement, your work based on -the Program is not required to print an announcement.) - -These requirements apply to the modified work as a whole. If -identifiable sections of that work are not derived from the Program, -and can be reasonably considered independent and separate works in -themselves, then this License, and its terms, do not apply to those -sections when you distribute them as separate works. But when you -distribute the same sections as part of a whole which is a work based -on the Program, the distribution of the whole must be on the terms of -this License, whose permissions for other licensees extend to the -entire whole, and thus to each and every part regardless of who wrote it. - -Thus, it is not the intent of this section to claim rights or contest -your rights to work written entirely by you; rather, the intent is to -exercise the right to control the distribution of derivative or -collective works based on the Program. - -In addition, mere aggregation of another work not based on the Program -with the Program (or with a work based on the Program) on a volume of -a storage or distribution medium does not bring the other work under -the scope of this License. - -3. You may copy and distribute the Program (or a work based on it, -under Section 2) in object code or executable form under the terms of -Sections 1 and 2 above provided that you also do one of the following: - -a) Accompany it with the complete corresponding machine-readable -source code, which must be distributed under the terms of Sections -1 and 2 above on a medium customarily used for software interchange; or, - -b) Accompany it with a written offer, valid for at least three -years, to give any third party, for a charge no more than your -cost of physically performing source distribution, a complete -machine-readable copy of the corresponding source code, to be -distributed under the terms of Sections 1 and 2 above on a medium -customarily used for software interchange; or, - -c) Accompany it with the information you received as to the offer -to distribute corresponding source code. (This alternative is -allowed only for noncommercial distribution and only if you -received the program in object code or executable form with such -an offer, in accord with Subsection b above.) - -The source code for a work means the preferred form of the work for -making modifications to it. For an executable work, complete source -code means all the source code for all modules it contains, plus any -associated interface definition files, plus the scripts used to -control compilation and installation of the executable. However, as a -special exception, the source code distributed need not include -anything that is normally distributed (in either source or binary -form) with the major components (compiler, kernel, and so on) of the -operating system on which the executable runs, unless that component -itself accompanies the executable. - -If distribution of executable or object code is made by offering -access to copy from a designated place, then offering equivalent -access to copy the source code from the same place counts as -distribution of the source code, even though third parties are not -compelled to copy the source along with the object code. - -4. You may not copy, modify, sublicense, or distribute the Program -except as expressly provided under this License. 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Each time you redistribute the Program (or any work based on the -Program), the recipient automatically receives a license from the -original licensor to copy, distribute or modify the Program subject to -these terms and conditions. You may not impose any further -restrictions on the recipients' exercise of the rights granted herein. -You are not responsible for enforcing compliance by third parties to -this License. - -7. If, as a consequence of a court judgment or allegation of patent -infringement or for any other reason (not limited to patent issues), -conditions are imposed on you (whether by court order, agreement or -otherwise) that contradict the conditions of this License, they do not -excuse you from the conditions of this License. If you cannot -distribute so as to satisfy simultaneously your obligations under this -License and any other pertinent obligations, then as a consequence you -may not distribute the Program at all. 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For software which is copyrighted by the Free -Software Foundation, write to the Free Software Foundation; we sometimes -make exceptions for this. Our decision will be guided by the two goals -of preserving the free status of all derivatives of our free software and -of promoting the sharing and reuse of software generally. - -NO WARRANTY - -11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY -FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN -OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES -PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED -OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF -MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS -TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE -PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, -REPAIR OR CORRECTION. - -12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING -WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR -REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, -INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING -OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED -TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY -YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER -PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE -POSSIBILITY OF SUCH DAMAGES. - -END OF TERMS AND CONDITIONS From 82adba8e2242ed9d6020152082d45f877dbdf928 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Fri, 19 Apr 2019 09:43:43 +0200 Subject: [PATCH 7/7] Update meta.yaml --- recipes/amap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/amap/meta.yaml b/recipes/amap/meta.yaml index 8a6019a31804e..931d508b81f49 100644 --- a/recipes/amap/meta.yaml +++ b/recipes/amap/meta.yaml @@ -27,10 +27,10 @@ test: about: home: https://web.archive.org/web/20060902044446/http://bio.math.berkeley.edu/amap/ license: GPL-2 - license_file: License.txt + license_file: license/License.txt summary: AMAP is a multiple sequence alignment program based on sequence annealing. dev_url: https://github.com/mes5k/amap-align extra: identifiers: - - doi:10.1093/bioinformatics/btl311 \ No newline at end of file + - doi:10.1093/bioinformatics/btl311