Comments (3)
Hi @kislyuk , I modified the install script in the install-iss36
branch to optionally work in two separate steps as you suggested, e.g.
./vadr-install.sh linux download
./vadr-install.sh build
Where linux
could alternatively be macosx
. The download step requires internet access but the build step does not (although it only works if the download step was already performed from the same directory).
The previous usage (e.g. ./vadr-install.sh linux
) still works also, and does both the download and build steps.
Please take a look and let me know if this is sufficient to make vadr easier to package for what you're interested in. Thanks.
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@nawrockie thank you so much, this is definitely an improvement! Dividing the install flow into two parts like this will allow us to download the dependency files in advance, and then install VADR into our Docker images reliably and reproducibly.
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@kislyuk , good, I'm glad this will be helpful. I've merged the install-iss36
branch with the main development branch (develop
) so this will go into the next release of vadr. I'm not sure of the timeframe though.
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Related Issues (20)
- ERROR in vdr_EutilsFetchToFile, problem fetching NC_063383.1 (undefined)
- ERROR in sqf_EslTranslateCdsToFastaFile, problem translating CDS feature, unable to find expected translated sequence in EU156171/EU156171.vadr.cds.esl-translate.2.fa: HOT 3
- Is there a database built for most viruses? HOT 2
- Bug in parse_blast.pl script causes max length deletion to be incorrectly reported in rare cases HOT 1
- Incorrect reporting of short frameshifts in 5' truncated CDS in rare cases HOT 1
- Bug: v-annotate.pl does not report cdsstopn for early in-frame stop codons in 3' truncated CDS if they are the final 3 nt of the input sequence HOT 3
- Bug: early stops misreported for multi-segment CDS HOT 1
- Bug: codon_start and truncation flag (<) missing in .tbl for multi-segment CDS if sequence begins after end of segment 1 HOT 1
- v-annotate.pl fails with 'unable to open file' error on mac os/x HOT 1
- Problem with building a model library HOT 4
- Installation Documentation: vadr-install.sh download link HOT 1
- Installation Issue 1.5.1 HOT 8
- Unable to build a model(NC_006273) HOT 1
- Bioconda - 1.6.3 broken symlink HOT 3
- compatibility with `-` and `.` in input assemblies HOT 2
- v-build.pl 1.6.3 fails on mac os/x HOT 1
- Extra header lines in .vadr.sqa HOT 2
- Outdated MODEL-VERSIONS.txt previnting automated model download HOT 2
- Frameshifts for 5' truncated alignments beginning with an insert are mishandled HOT 1
- v-annotate.pl bug: cdsstopp alert causes script to fail if early stop position exceeds CDS model length HOT 2
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