https://github.com/cpanse/koina-rclient
R lang client for koina (DLOmix) service
Science Score: 13.0%
This score indicates how likely this project is to be science-related based on various indicators:
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○CITATION.cff file
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✓codemeta.json file
Found codemeta.json file -
○.zenodo.json file
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○DOI references
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○Academic publication links
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○Academic email domains
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○Institutional organization owner
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○JOSS paper metadata
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○Scientific vocabulary similarity
Low similarity (6.6%) to scientific vocabulary
Keywords
Repository
R lang client for koina (DLOmix) service
Basic Info
- Host: GitHub
- Owner: cpanse
- Language: C++
- Default Branch: main
- Homepage: https://koina.proteomicsdb.org/
- Size: 4.13 MB
Statistics
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
- Releases: 0
Topics
Metadata Files
README.md
Rpkg client for the koina.proteomicsdb.org service
FAQ
What is Koina?
read: https://koina.proteomicsdb.org/
how to run the server?
Option 1
follow the install: github.com:wilhelm-lab/koina.git
docker compose up serving -d
docker compose logs serving -f
Option 2
use a public one, e.g., dlomix.fgcz.uzh.ch:8080 (using usessl=FALSE)
or koina.proteomicsdb.org:443
how to set the library path?
``` $ export LDLIBRARYPATH=$LDLIBRARYPATH:$HOME/src/v2.34.0dev.clients/lib/
cpanse@fgcz-h-480:~/src/github.com/cpanse/dlomix-Rclient (main)> ldd dlomix linux-vdso.so.1 (0x00007ffcbfba0000) libgrpcclient.so => /home/cpanse/src/v2.34.0dev.clients/lib/libgrpcclient.so (0x00007fa98cd29000) libstdc++.so.6 => /lib/x8664-linux-gnu/libstdc++.so.6 (0x00007fa98cb51000) libgccs.so.1 => /lib/x8664-linux-gnu/libgccs.so.1 (0x00007fa98cb37000) libc.so.6 => /lib/x8664-linux-gnu/libc.so.6 (0x00007fa98c962000) libz.so.1 => /lib/x8664-linux-gnu/libz.so.1 (0x00007fa98c945000) libssl.so.1.1 => /lib/x8664-linux-gnu/libssl.so.1.1 (0x00007fa98c8b2000) libcrypto.so.1.1 => /lib/x8664-linux-gnu/libcrypto.so.1.1 (0x00007fa98c5bb000) libpthread.so.0 => /lib/x8664-linux-gnu/libpthread.so.0 (0x00007fa98c599000) libm.so.6 => /lib/x8664-linux-gnu/libm.so.6 (0x00007fa98c455000) /lib64/ld-linux-x86-64.so.2 (0x00007fa98d654000) libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00007fa98c44f000)
``` see also INSTALL
how to set the right data type?
https://github.com/triton-inference-server/server/blob/main/docs/userguide/modelconfiguration.md
how to get the Rcpp example to work?
```
R
otherwise the library can not resolve all entries!
Sys.setenv("PKGCXXFLAGS"="-I/home/cpanse/src/v2.34.0dev.clients/include/ -Wall -pedantic -std=c++17 -O3") Sys.setenv("PKGLIBS"="-L /home/cpanse/src/v2.34.0dev.clients/lib/ -lgrpcclient")
Rcpp::sourceCpp("src/rcpp_alphapept.cpp ", verbose = TRUE, rebuild = TRUE, cacheDir = "dlomixRcpp")
call
out <- dlomixAlphaPeptms2genericensemble("ELVISK") ``` of note, this section is outdated
links
- https://github.com/eubic/EuBIC2023/issues/12
Owner
- Name: Christian Panse
- Login: cpanse
- Kind: user
- Location: 47N 008E
- Company: Swiss federal institute of technology in Zurich
- Website: https://fgcz.ch/compms
- Repositories: 72
- Profile: https://github.com/cpanse
proteome informatics; ms comp; visualization; maps; code; reproducible research @hb9feb@fosstodon.org
GitHub Events
Total
Last Year
Issues and Pull Requests
Last synced: 11 months ago
All Time
- Total issues: 2
- Total pull requests: 0
- Average time to close issues: 3 months
- Average time to close pull requests: N/A
- Total issue authors: 1
- Total pull request authors: 0
- Average comments per issue: 0.5
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- cpanse (1)