bacarson/SLiM-Selection_on_Linked_Mutations

Project ID: 36861

Description

SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. Simulations are configured via the integrated Eidos scripting language that allows interactive control over practically every aspect of the simulated evolutionary scenarios. The underlying individual-based simulation engine is highly optimized to enable modeling of entire chromosomes in large populations. We also provide a graphical user interface on macOS and Linux for easy simulation set-up, interactive runtime control, and dynamical visualization of simulation output.

Installation Instructions

Fedora, Red Hat Enterprise Linux, CentOS: Enable the COPR repository then install using DNF.

sudo dnf copr enable bacarson/SLiM-Selection_on_Linked_Mutations
sudo dnf install SLiM

openSUSE, SUSE Linux Enterprise: Add the repository to your system, then refresh the package list and install using Zypper.

Copy the link address of the Zypper repository to your system clipboard by right-clicking on the button in the distribution table below, then select "Copy link address"
Add the repository to the Zypper repository list by executing this command in a terminal: sudo zypper ar <PASTE the repository URL here>
Update the packages known to Zypper sudo zypper refresh
Install SLiM sudo zypper install SLiM

openSUSE Leap 15.4: As Fedora Copr does not yet have a chroot for this distribution version, it could not be built automatically from upstream sources along with the rest of the supported RPM-based distributions. The RPM was built manually from the same upstream sources, and is downloadable from Packagecloud. This RPM is shipped without a Zypper repository for automatic updates. Users of this package must manually check for updates here or on #slim-announce or GitHub until an announcement is made for this distribution recieving a Zypper repository.

Instructions for using the RPM:

Download the RPM
Click the RPM in the folder where it was saved by the web browser, YaST Software Install should open \
Follow the YaST wizard and install the package

Please note that this package, SLiM, conflicts with Simple Login Manager, which is packaged and distributed from the official Fedora repository as slim. This conflict is being discussed and will be resolved in the future.

On RedHat Enterprise Linux 8, the EPEL 8 repository with the CentOS logo is compatible, as RHEL is the upstream of CentOS; enabling the COPR repository as instructed above should work; if it doesn't work, please try the .repo file or the .rpm directly and if that fails contact Bryce Carson.

Mailing Lists

There are two mailing lists. Please subscribe to either or both using the links below:

slim-announce: A low-volume mailing list for announcements only. Users may not post to this list.
slim-discuss: A higher-volume mailing list for questions, comments, bug reports, and discussion among users of SLiM.

Reporting Package Issues

Issues with installation or package dependencies should be directed to Bryce Carson (bryce.a.carson@gmail.com). Please use a subject line of: SLiM-Packaging: [Distribution (E.g. RHEL 8)].

Examples of packaging issues:

The package fails to install
Dependencies for SLiM cannot be satisfied with the default repositories in the distribution of choice
Desktop integration issues

All other issues should be directed to the slim-discuss mailing list or the upstream developer's GitHub.

Changelog

4.0.1-1 Tue Sep 13 2022, Ben Haller (bhaller@mac.com)

Final candidate 1 for 4.0.1 release

4.0-2 Tue Aug 23 2022, Bryce Carson (bryce.a.carson@gmail.com)

Include new changelog entry to identify the date of the new release

4.0-1 Wed Aug 10 2022, Bryce Carson (bryce.a.carson@gmail.com)

New release

3.7.1-1 Sat Feb 12 2022, Bryce Carson (bryce.a.carson@gmail.com)

Increment version

3.7-1 Wed Dec 15 2021, Ben Haller (bhaller@mac.com)

Final candidate 1 for 3.7 release
Removed robinhood patch
Removed --parallel for cmake since it was no longer working

3.6-5 Sat Apr 24 2021, Bryce Carson (bryce.a.carson@gmail.com)

Fixed email address in previous changelog entry.
Included a conflict tag to prevent users of this package from using the conflicting binary in Simple Login Manager.

3.6-4 Sat Mar 20 2021, Bryce Carson (bryce.a.carson@gmail.com)

Added support for openSUSE (with SUSE Linux Enterprise users possibly able to use the openSUSE RPM).
Cleaned up the changelog.
The [<jobs>] argument to the cmake --parallel option was removed, so that Copr uses the default number of concurrent processes (and hopefully the maximum number, rather than hardcoding eight processes).

3.6-3 Wed Mar 3 2021, Bryce Carson (bryce.a.carson@gmail.com)

Application of patch to allow building on Fedora 34 and Fedora Rawhide.

3.6-2 Wed Mar 3 2021, Bryce Carson (bryce.a.carson@gmail.com)

Specified required Qt 5.15.2 on Fedora 34.
Added package version in previous changelog entry.

3.6-1 Wed Mar 3 2021, Bryce Carson (bryce.a.carson@gmail.com)

New package release.
Removed source edits that were addressed upstream.

3.5-6 Sun Jan 31 2021, Bryce Carson (bryce.a.carson@gmail.com)

spec file improvements; brace expansion used and sorting performed.
FreeDesktop compliance improvements; the organization domain and application name are corrected and are now compliant.
Source modifications allow Gnome Classic to display the proper application name. -- Te symbolic application icon is now created programmatically from upstream icons in the source, rather than a second source file.

3.5-5 Thu Jan 28 2021, Bryce Carson (bryce.a.carson@gmail.com)

org.messerlab.slimgui.desktop changed in prep to correct Categories value; fixes desktop integration on Fedora 33 when using Gnome Classic environment.
New symbolic icon included; improves desktop integration on Fedora 33 when using Gnome 3 with Wayland.
Edited the changelog to not refer to the prep stage as a macro, simply "prep", to fix rpmlint warnings.

3.5-4 Thu Jan 14 2021, Bryce Carson (bryce.a.carson@gmail.com)

org.messerlab.slimgui.desktop changed in prep to correct StartupWMClass and icon; fixes desktop integration on Fedora 33.
Sorted changelog in descending chronological order.

3.5-3 Sun Dec 06 2020, Bryce Carson (bryce.a.carson@gmail.com)

Updated the requires in the .spec file (and thus the package dependencies) to reflect updates to Qt5 on Fedora 33.
Qt5 5.15.2 now required on Fedora 33.

3.5-2 Unreleased, Bryce Carson (bryce.a.carson@gmail.com)

Changed the tar command in .spec file to address discrepancy between GitHub archive URI and downloaded source archive.

3.5-1 Unreleased, Bryce Carson (bryce.a.carson@gmail.com)

Created new release package
Differences from 3.4-8 include removal of necessary source modifications for 3.4
The source modifications for 3.4 were addressed by the upstream

Active Releases

The following unofficial repositories are provided as-is by owner of this project. Contact the owner directly for bugs or issues (IE: not bugzilla).

Release	Architectures	Repo Download
Centos-stream 8	x86_64 (0)*	Centos-stream 8 (142 downloads)
Centos-stream 9	x86_64 (2)*	Centos-stream 9 (36 downloads)
EPEL 8	x86_64 (6)*	EPEL 8 (166 downloads)
Fedora 35	x86_64 (7)*	Fedora 35 (0 downloads)
Fedora 36	x86_64 (19)*	Fedora 36 (0 downloads)
Fedora 37	x86_64 (13)*	Fedora 37 (20 downloads)
Fedora 38	x86_64 (8)*	Fedora 38 (7 downloads)
Fedora rawhide	x86_64 (1)*	Fedora rawhide (143 downloads)
openSUSE Leap 15.3	x86_64 (0)*	openSUSE Leap 15.3 (27 downloads)
openSUSE Tumbleweed	x86_64 (12)*	openSUSE Tumbleweed (130 downloads)