sci-biology/snapgene-viewer: New package

Signed-off-by: Pacho Ramos <pacho@gentoo.org>

4 files changed, 299 insertions, 0 deletions

diff --git a/licenses/GSL b/licenses/GSL
new file mode 100644
index 000000000..38014b153
--- /dev/null
+++ b/licenses/GSL
@@ -0,0 +1,221 @@
+   END USER LICENSE AGREEMENT
+
+   NOTICE: THIS SOFTWARE END USER LICENSE AGREEMENT ("EULA") IS A LEGAL
+   AGREEMENT BETWEEN YOU (EITHER AS AN INDIVIDUAL OR AN ENTITY) AND GSL
+   BIOTECH LLC ("GSL"). PLEASE READ IT CAREFULLY BEFORE COMPLETING THE
+   INSTALLATION PROCESS AND USING THE SOFTWARE. THIS AGREEMENT PROVIDES A
+   LICENSE TO USE THE SOFTWARE AND CONTAINS WARRANTY INFORMATION AND
+   LIABILITY DISCLAIMERS. BY INSTALLING AND USING THE SOFTWARE, YOU ARE
+   CONFIRMING YOUR ACCEPTANCE OF THE SOFTWARE AND AGREEING TO BECOME BOUND BY
+   THE TERMS OF THIS AGREEMENT. IF YOU DO NOT AGREE TO BE BOUND BY THESE
+   TERMS, THEN DO NOT INSTALL THE SOFTWARE, AND RETURN THE SOFTWARE TO GSL.
+
+    1. Recitals
+
+         1. This End User License Agreement ("EULA") is a legal agreement
+            between you (either an individual person or a single legal
+            entity, who will be referred to in this EULA as "End User", and
+            GSL Biotech LLC ("GSL") for the SnapGene software product
+            ("Software") or SnapGene Viewer software product ("Freeware")
+            that accompanies this EULA, including any associated media,
+            printed materials and electronic documentation.
+         2. The Software or Freeware also includes any software updates,
+            add-on components, web services and/or supplements that GSL may
+            provide to End User or make available to End User after the date
+            End User obtains the initial copy of the Software or Freeware, to
+            the extent that such items are not accompanied by a separate
+            license agreement or terms of use. By installing, copying,
+            downloading, accessing or otherwise using the Software or
+            Freeware, End User agrees to be bound by the terms of this EULA.
+            If End User does not agree to the terms of this EULA, End User
+            should not install, access or use the Software or Freeware.
+
+    2. License Grants
+
+         1. Freeware License. GSL grants End User an unlimited license to use
+            the Freeware. The install packages for the Freeware can be
+            redistributed without restriction, and can be used for both
+            commercial and non-commercial purposes.
+         2. Trial Period License. End User may download and use the Software
+            for free for thirty (30) days after installation ("Trial
+            Period"). During the Trial Period, GSL grants End User a limited,
+            non-exclusive, non-transferable, non-renewable license to copy
+            and use the Software for evaluation purposes only. At GSL's
+            discretion, GSL may provide limited support through email or
+            discussion forums at GSL's website. The evaluation copy of the
+            Software contains a feature that will automatically disable
+            certain features of the Software at the end of Trial Period. GSL
+            will have no liability to End User if this feature disables the
+            Software.
+         3. License After Trial Period. This Software is licensed, not sold.
+            End User has the option of paying a license fee in order to use
+            the Software after the expiration of the Trial Period. Upon
+            payment of the license fee, GSL provides End User with a
+            registration number, and grants End User a limited,
+            non-exclusive, non-transferable license as outlined in Sections
+            2.d through Section 2.g and in Section 3.
+         4. Computer-Specific License. Under the terms of a Computer-Specific
+            License for the Software, End User may activate each license only
+            on a single computer, and may use the Software only on that
+            computer. The Software may not be accessed remotely.
+         5. Floating License. Under the terms of a Floating License for the
+            Software, End User may install the Software on an unlimited
+            number of computers. All computers using the Software must have
+            the ability to communicate with a license server. The number of
+            users who may run the Software concurrently must not at any time
+            exceed the number of Floating Licenses purchased.
+         6. Unlimited License. Under the terms of an Unlimited License for
+            the Software, End User may install and use the Software on an
+            unlimited number of computers with IP addresses in a specified IP
+            range as agreed to by GSL and End User.
+         7. The Software or Freeware is for educational and non-commercial or
+            commercial research purposes only. GSL makes no representation
+            that the Software or Freeware is a clinically approved medical
+            device, and End User understands and accepts that any result or
+            its display presented in whatever form obtained using the
+            Software or Freeware must not be used for any purpose other than
+            education or research.
+
+    3. License Restrictions
+
+         1. End User may use the Software only on the permitted number of
+            computers.
+         2. End User may make one copy of the Software solely for backup
+            purposes. Any backup copy must contain all copyright notices and
+            any other proprietary legends on the original copy of the
+            Software. End User may not sell or transfer any copy of the
+            Software made for backup purposes.
+         3. End User's license rights under this EULA are non-exclusive and
+            non-assignable.
+         4. Other than as set forth in Section 3.b, End User may not make
+            copies of the Software or electronically transfer the Software
+            from one computer to another.
+         5. End User may not alter, merge, modify, adapt, translate,
+            decompile, reverse engineer, disassemble, or otherwise reduce the
+            Software to a human-perceivable form.
+         6. End User may not rent, lease, or sublicense the Software.
+         7. End User may not create derivative works based upon the Software.
+         8. End User may not export the Software into any country to which
+            such export is prohibited by the United States Export
+            Administration Act.
+         9. In the event that End User fails to comply with this EULA, GSL
+            and its distributors may, in addition to seeking any damages,
+            terminate the license. Upon termination, End User must destroy
+            all copies of the Software (with all other rights of both parties
+            and all other provisions of this EULA surviving any such
+            termination).
+
+    4. Ownership
+
+       The foregoing license gives End User a limited license to use the
+       Software. GSL retains all rights, title and interest, including all
+       copyright and intellectual property rights, in and to the Software and
+       all copies thereof. The Software is protected by the copyright laws of
+       the United States and other countries. All rights not expressly
+       granted in this EULA are reserved by GSL.
+
+    5. LIMITED WARRANTY AND DISCLAIMER
+
+         1. GSL warrants that, for a period of ninety (90) days, the Software
+            will perform in substantial conformance with published
+            specifications for the Software.
+         2. EXCEPT AS SET FORTH IN THE FOREGOING LIMITED WARRANTY WITH
+            RESPECT TO THE SOFTWARE, GSL DISCLAIMS ALL OTHER WARRANTIES AND
+            REPRESENTATIONS, WHETHER EXPRESS, IMPLIED, OR OTHERWISE,
+            INCLUDING THE WARRANTIES OF MERCHANTABILITY OR FITNESS FOR A
+            PARTICULAR PURPOSE. ALSO, THERE IS NO WARRANTY OF
+            NON-INFRINGEMENT AND TITLE OR QUIET ENJOYMENT. GSL DOES NOT
+            WARRANT THAT THE SOFTWARE IS ERROR-FREE OR WILL OPERATE WITHOUT
+            INTERRUPTION. THE SOFTWARE IS NOT DESIGNED, INTENDED OR LICENSED
+            FOR USE IN HAZARDOUS ENVIRONMENTS REQUIRING FAIL-SAFE CONTROLS.
+         3. IF APPLICABLE LAW REQUIRES ANY WARRANTIES WITH RESPECT TO THE
+            SOFTWARE, ALL SUCH WARRANTIES ARE LIMITED IN DURATION TO NINETY
+            (90) DAYS FROM THE DATE OF DELIVERY.
+         4. NO ORAL OR WRITTEN INFORMATION OR ADVICE GIVEN BY GSL SHALL
+            CREATE A WARRANTY OR IN ANY WAY INCREASE THE SCOPE OF ANY
+            WARRANTY PROVIDED HEREIN.
+         5. (USA only) SOME STATES DO NOT ALLOW THE EXCLUSION OF IMPLIED
+            WARRANTIES, SO THE ABOVE EXCLUSION MAY NOT APPLY TO END USER.
+            THIS WARRANTY GIVES END USER SPECIFIC LEGAL RIGHTS AND END USER
+            MAY ALSO HAVE OTHER LEGAL RIGHTS THAT VARY FROM STATE TO STATE.
+
+    6. Exclusive Remedy
+
+       End User's exclusive remedy is to return the Software to GSL. Provided
+       that any non-compliance with the above warranty is reported in writing
+       to GSL no more than ninety (90) days following delivery to End User,
+       GSL will use reasonable commercial efforts to supply End User with a
+       replacement copy of the Software that substantially conforms to
+       published specifications, provide a replacement for defective media,
+       or refund to End User the purchase price for the Software, at its
+       option. GSL shall have no responsibility if the Software has been
+       altered in any way, or if the media has been damaged by misuse,
+       accident, abuse, modification or misapplication. Any such misuse,
+       accident, abuse, modification or misapplication of the Software will
+       void the warranty above. THIS REMEDY IS THE SOLE AND EXCLUSIVE REMEDY
+       AVAILABLE TO END USER FOR BREACH OF EXPRESS OR IMPLIED WARRANTIES WITH
+       RESPECT TO THE SOFTWARE.
+
+    7. LIMITATION OF LIABILITY
+
+         1. GSL SHALL NOT BE LIABLE TO END USER OR ANY THIRD PARTY FOR ANY
+            INDIRECT, SPECIAL, INCIDENTAL, PUNITIVE, COVER OR CONSEQUENTIAL
+            DAMAGES (INCLUDING, BUT NOT LIMITED TO, DAMAGES FOR THE INABILITY
+            TO USE EQUIPMENT OR ACCESS DATA, LOSS OF BUSINESS, LOSS OF
+            PROFITS, BUSINESS INTERRUPTION OR THE LIKE), ARISING OUT OF THE
+            USE OF, OR INABILITY TO USE, THE SOFTWARE AND BASED ON ANY THEORY
+            OF LIABILITY INCLUDING BREACH OF CONTRACT, BREACH OF WARRANTY,
+            TORT (INCLUDING NEGLIGENCE), PRODUCT LIABILITY OR OTHERWISE, EVEN
+            IF GSL OR ITS REPRESENTATIVES HAVE BEEN ADVISED OF THE
+            POSSIBILITY OF SUCH DAMAGES AND EVEN IF A REMEDY SET FORTH HEREIN
+            IS FOUND TO HAVE FAILED IN ITS ESSENTIAL PURPOSE.
+         2. GSL'S TOTAL LIABILITY TO END USER FOR ACTUAL DAMAGES FOR ANY
+            CAUSE WHATSOEVER WILL BE LIMITED TO THE AMOUNT END USER PAID FOR
+            THE SOFTWARE.
+         3. (USA only) SOME STATES DO NOT ALLOW THE LIMITATION OR EXCLUSION
+            OF LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES, SO THE
+            ABOVE LIMITATION OR EXCLUSION MAY NOT APPLY TO END USER AND END
+            USER MAY ALSO HAVE OTHER LEGAL RIGHTS THAT VARY FROM STATE TO
+            STATE.
+         4. THE FOREGOING LIMITATIONS ON LIABILITY ARE INTENDED TO APPLY TO
+            THE WARRANTIES AND DISCLAIMERS ABOVE AND ALL OTHER ASPECTS OF
+            THIS EULA.
+
+    8. U.S. GOVERNMENT RESTRICTED RIGHTS LEGEND
+
+       This Software and the documentation are provided with "RESTRICTED
+       RIGHTS" applicable to private and public licenses alike. Without
+       limiting the foregoing, use, duplication, or disclosure by the U.S.
+       Government is subject to restrictions as set forth in this EULA and as
+       provided in DFARS 227.7202-1(a) and 227.7202-3(a) (1995), DFARS
+       252.227-7013 (c)(1)(ii)(OCT 1988), FAR 12.212(a)(1995), FAR 52.227-19,
+       or FAR 52.227-14, as applicable. Manufacturer: GSL Biotech LLC
+
+    9. General
+
+       This EULA shall be governed by the internal laws of the State of
+       Illinois, USA. In each case this EULA shall be construed and enforced
+       without regard to the United Nations Convention on the International
+       Sale of Goods.
+
+       This EULA contains the complete agreement between the parties with
+       respect to the subject matter hereof, and supersedes all prior or
+       contemporaneous agreements or understandings, whether oral or written.
+       End User agrees that any varying or additional terms contained in any
+       purchase order or other written notification or document issued by End
+       User in relation to the Software licensed hereunder shall be of no
+       effect. The failure or delay of GSL to exercise any of its rights
+       under this EULA or upon any breach of this EULA shall not be deemed a
+       waiver of those rights or of the breach.
+
+       If any provision of this EULA shall be held by a court of competent
+       jurisdiction to be contrary to law, then that provision will be
+       enforced to the maximum extent permissible and the remaining
+       provisions of this EULA will remain in full force and effect.
+
+       All questions concerning this EULA shall be directed to GSL. This EULA
+       does not authorize End User to use the trademarks of GSL or its
+       suppliers.
+
+   GSL Biotech LLC
+   July 18th, 2017
diff --git a/sci-biology/snapgene-viewer/Manifest b/sci-biology/snapgene-viewer/Manifest
new file mode 100644
index 000000000..2e6582002
--- /dev/null
+++ b/sci-biology/snapgene-viewer/Manifest
@@ -0,0 +1 @@
+DIST snapgene_7.0.3_linux.deb 129706720 BLAKE2B 539257921cc36c8770f5786e3af37502a6e958636ed32f861dcb2fd4621dfbac19d39c9a0772e0d08a532226f9b1875964bf657638917b52c606ff448a03b6f3 SHA512 b902d2bc229e697c4409b09b4f8e2a0ef6583a1958e7a38ef8321b453cdda687e33bc42adb14133d7320cc18791ec1b79409701efbfc5f6be0bbcce2f4e6e87f
diff --git a/sci-biology/snapgene-viewer/metadata.xml b/sci-biology/snapgene-viewer/metadata.xml
new file mode 100644
index 000000000..5c83ce208
--- /dev/null
+++ b/sci-biology/snapgene-viewer/metadata.xml
@@ -0,0 +1,12 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="person">
+		<email>pacho@gentoo.org</email>
+		<name>Pacho Ramos</name>
+	</maintainer>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild
new file mode 100644
index 000000000..d117fbc14
--- /dev/null
+++ b/sci-biology/snapgene-viewer/snapgene-viewer-7.0.3.ebuild
@@ -0,0 +1,65 @@
+# Copyright 2023 Gentoo Authors
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=8
+inherit unpacker wrapper xdg
+
+DESCRIPTION="Software for plasmid mapping, primer design, and restriction site analysis"
+HOMEPAGE="https://www.snapgene.com/features"
+SRC_URI="snapgene_${PV}_linux.deb"
+SNAPGENE_DOWNLOAD="https://www.snapgene.com/local/targets/download.php?os=linux_deb&variant=paid&release=${PV}"
+RESTRICT="fetch"
+
+LICENSE="GSL"
+SLOT="0"
+KEYWORDS="~amd64"
+
+DEPEND=""
+# ldd /opt/gslbiotech/snapgene/snapgene
+RDEPEND="${DEPEND}
+	app-arch/bzip2
+	app-arch/xz-utils
+	app-crypt/qca[qt6]
+	dev-libs/openssl-compat:1.1.1
+	dev-qt/qt5compat:6
+	dev-qt/qtbase:6[concurrent,gui,network,opengl,sql,widgets,xml]
+	dev-qt/qtdeclarative:6
+	dev-qt/qtpositioning:6
+	dev-qt/qtwebchannel:6
+	dev-qt/qtwebengine:6
+	media-libs/libglvnd
+	media-libs/tiff-compat:4
+	sci-libs/htslib:0/3
+	sys-devel/gcc
+	sys-libs/glibc
+	sys-libs/libcxx[libcxxabi]
+	sys-libs/libunwind:0/8
+	x11-libs/libX11
+	x11-libs/libXau
+	x11-libs/libXdmcp
+	x11-libs/libxcb
+"
+BDEPEND=">=dev-util/patchelf-0.10"
+
+S="${WORKDIR}"
+QA_PREBUILT="*"
+
+pkg_nofetch() {
+	elog "Please download ${SRC_URI} from"
+	elog "${SNAPGENE_DOWNLOAD}"
+	elog "and place it into your DISTDIR directory."
+}
+
+src_install() {
+	patchelf --replace-needed libunwind.so.1 libunwind.so.8 \
+		opt/gslbiotech/snapgene/snapgene || die
+
+	mv usr/share/doc/snapgene usr/share/doc/${PF} || die
+	gzip -d usr/share/doc/${PF}/changelog.Debian.gz || die
+
+	insinto /
+	doins -r *
+
+	fperms +x /opt/gslbiotech/snapgene/snapgene{,.sh}
+	make_wrapper ${PN} ./snapgene.sh /opt/gslbiotech/snapgene/
+}