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https://github.com/cpanse/koina-rclient
Rpkg client for koina (DLOmix) service
https://github.com/cpanse/koina-rclient
computational-mass-spectrometry deep-learning fun grpc-client
Last synced: 18 days ago
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Rpkg client for koina (DLOmix) service
- Host: GitHub
- URL: https://github.com/cpanse/koina-rclient
- Owner: cpanse
- Created: 2023-04-29T17:53:41.000Z (over 1 year ago)
- Default Branch: main
- Last Pushed: 2023-09-25T08:42:22.000Z (over 1 year ago)
- Last Synced: 2023-09-25T15:15:45.347Z (over 1 year ago)
- Topics: computational-mass-spectrometry, deep-learning, fun, grpc-client
- Language: C++
- Homepage: https://koina.proteomicsdb.org/
- Size: 4.13 MB
- Stars: 2
- Watchers: 1
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# 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 LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$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/x86_64-linux-gnu/libstdc++.so.6 (0x00007fa98cb51000)
libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00007fa98cb37000)
libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00007fa98c962000)
libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00007fa98c945000)
libssl.so.1.1 => /lib/x86_64-linux-gnu/libssl.so.1.1 (0x00007fa98c8b2000)
libcrypto.so.1.1 => /lib/x86_64-linux-gnu/libcrypto.so.1.1 (0x00007fa98c5bb000)
libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 (0x00007fa98c599000)
libm.so.6 => /lib/x86_64-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](INSTALL)
### how to set the right data type?
https://github.com/triton-inference-server/server/blob/main/docs/user_guide/model_configuration.md
### how to get the Rcpp example to work?
```
#R
## otherwise the library can not resolve all entries!
Sys.setenv("PKG_CXXFLAGS"="-I/home/cpanse/src/v2.34.0dev.clients/include/ -Wall -pedantic -std=c++17 -O3")
Sys.setenv("PKG_LIBS"="-L /home/cpanse/src/v2.34.0dev.clients/lib/ -lgrpcclient")
Rcpp::sourceCpp("src/rcpp_alphapept.cpp ", verbose = TRUE, rebuild = TRUE, cacheDir = "dlomixRcpp")
## call
out <- dlomix_AlphaPept_ms2_generic_ensemble("ELVISK")
```
of note, this section is outdated
## links
- https://github.com/eubic/EuBIC2023/issues/12