Package Details: snapgene 8.0.1-2

Git Clone URL: https://aur.archlinux.org/snapgene.git (read-only, click to copy)
Package Base: snapgene
Description: Software for plasmid mapping, primer design, and restriction site analysis
Upstream URL: https://www.snapgene.com/about
Keywords: biology cloning design dna molecular plasmid primer snapgene
Licenses: custom
Submitter: Ezmagon
Maintainer: Bitals
Last Packager: Bitals
Votes: 4
Popularity: 0.000140
First Submitted: 2018-09-19 12:48 (UTC)
Last Updated: 2024-11-25 20:59 (UTC)

Latest Comments

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Bitals commented on 2024-06-28 10:01 (UTC)

@fdecarpentier thank you, fixed.

fdecarpentier commented on 2024-06-28 00:23 (UTC)

Dear Bitals, thank you for maintaining this package. TLDR : openmp dependency is missing

The DNA and protein alignment tools throw this error : " /opt/gslbiotech/snapgene/resources/Tools/parasail/parasail_aligner: error while loading shared libraries: libomp.so: cannot open shared object file: No such file or directory " I fixed this by installing openmp through pacman.

Bitals commented on 2024-04-08 10:00 (UTC)

@Kiri0 thank you for your input. About binary rpath - it's purely a cosmetic issue as the /opt/gslbiotech/snapgene/snapgene.sh (script that is ran by /usr/bin/snapgene, hence it shouldn't be renamed to snapgene.sh for differentiation and ease of CLI launch purposes, but I agree this is pretty janky) sets the LD_LIBRARY_PATH to the correct directory, allowing the binary to use the libraries there. I tried to merge these 2 scripts before, but didn't get something to work and postponed this to sometime(tm). In other words - there's a lot of polishing to be done in the startup area, which I will get to eventually.

About the license install method - thanks, I see no problem with implementing this change, will do this before or with the next release, which I guess might come towards the end of the month.

Kiri0 commented on 2024-04-01 10:42 (UTC) (edited on 2024-04-01 10:43 (UTC) by Kiri0)

Maybe rename the "snapgene" to "snapgene.sh" and use this way to install the "LICENSE" and "/usr/bin/snapgene"

install -Dm 755 "$srcdir/snapgene.sh" "$pkgdir/usr/bin/snapgene"
install -Dm 664 "$pkgdir/opt/gslbiotech/snapgene/resources/licenseAgreement.html" "$pkgdir/usr/share/licenses/$pkgname/LICENSE.html"

So that don't need mkdir nor chmod.

Same to snapgene-viewer.

Kiri0 commented on 2024-04-01 08:15 (UTC) (edited on 2024-04-01 08:16 (UTC) by Kiri0)

some .so and snapgene(bin) contain rpath of "/home/centos/*" only. It may be mistake by upstream while building. 

snapgene E: Insecure RPATH '/home/centos/.conan/data/qt-for-sg/6.2.10/snapgene/stable/package/f6a1919c5d86e9463ebddc2f3d4066e8e92eadce/lib' in file ('opt/gslbiotech/snapgene/libqntp.so.1.0.0')
snapgene E: Insecure RPATH '/home/centos/.conan/data/qt-for-sg/6.2.10/snapgene/stable/package/f6a1919c5d86e9463ebddc2f3d4066e8e92eadce/lib' in file ('opt/gslbiotech/snapgene/libqwebdavlib.so.1.0.0')

This should fix it(add "patchelf" to makedepends):

    # Fix rpath which cause "Insecure RUNPATH" or "outside of a valid path"
    # Fix .so files using patchelf
    cd "${pkgdir}/opt/gslbiotech/snapgene"
    for file in *.so*; do
        PATCHELF_OUTPUT=$(patchelf --print-rpath $file)
        echo "Checking $file: $PATCHELF_OUTPUT"
    # Skip file if PATCHELF_OUTPUT does not contain CURRENT_DIR
        if [[ ! $PATCHELF_OUTPUT =~ "/home" ]]; then
            echo "Skipping $file"
            continue
        fi
    # Remove rpath if it not contain ORIGIN before
        if [[ ! $PATCHELF_OUTPUT =~ 'ORIGIN' ]]; then
            echo "Removing rpath for $file"
            patchelf --remove-rpath $file
            continue
        fi
    # Set rpath to ORIGIN if it contain ORIGIN before
        echo "Setting ORIGIN rpath for $file"
        patchelf --set-rpath '$ORIGIN' $file
    done

    # Remove rpath of snapgene
    echo "Removing rpath for snapgene"
    patchelf --remove-rpath snapgene

same as snapgene-viewer

Bitals commented on 2023-12-29 07:30 (UTC) (edited on 2023-12-29 07:31 (UTC) by Bitals)

@Kiri0 Ezmagon has stepped down from maintaining this package, I took it over. Both Snapgene and Snapgene Viewer PKGBUILDS are on my Github: https://github.com/Bitals?tab=repositories Feel free to include a submodule in your Repo, it's not like I hold a Copyright on Snapgene the software, PKGBUILD itself is FOSS and you do not need permission to do anything with it.

Kiri0 commented on 2023-12-29 04:28 (UTC)

Hi @Ezmagon, this very helpful! and I introduce a bio-softs repo: BioArchlinux, if you are interested in, feel free to join! we are try to collect all bio-softs as much as we can.

Bitals commented on 2022-08-17 08:10 (UTC)

It is possible to grab the needed rpm directrly from their CDN with this unholy variable mess (works for 5.0.7 still, they keep hosting it):

_pkgver_major=$(cut -d '.' -f 1 <<<"$pkgver")
_pkgver_major_middle=$(cut -d '.' -f 1-2 <<<"$pkgver")
source=("https://cdn.snapgene.com/downloads/SnapGene/"$_pkgver_major".x/"$_pkgver_major_middle"/"$pkgver"/snapgene_"$pkgver"_linux.rpm")

carlosal1015 commented on 2022-01-25 15:33 (UTC)

Hi @Ezmagon, would you like to merge this package with yours.

boina commented on 2020-04-27 17:02 (UTC)

Nice!! Thanks a lot. Works like a charm. I modified the PKBUILD to install the beta version 5.1 When I opened snapgene I got a warning of the font Verdana not present in the system but it works just fine without it. Perhaps you may want to add the package "ttf-ms-fonts" as an optional dependency.

By the way, I use gnome.

José.

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