Skip to content

Instantly share code, notes, and snippets.

View jpfeuffer's full-sized avatar
:octocat:

Julianus Pfeuffer jpfeuffer

:octocat:
32 followers · 4 following
View GitHub Profile
@jpfeuffer
jpfeuffer / pyopenms_pandas.ipynb
Created September 6, 2021 16:59
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
@jpfeuffer
jpfeuffer / newplfq.log
Created May 19, 2021 14:43
UpdateCTestConfiguration from :/Users/pfeuffer/git/OpenMS-fixes-src/cmake-build-debug/DartConfiguration.tcl
Parse Config file:/Users/pfeuffer/git/OpenMS-fixes-src/cmake-build-debug/DartConfiguration.tcl
UpdateCTestConfiguration from :/Users/pfeuffer/git/OpenMS-fixes-src/cmake-build-debug/DartConfiguration.tcl
Parse Config file:/Users/pfeuffer/git/OpenMS-fixes-src/cmake-build-debug/DartConfiguration.tcl
Test project /Users/pfeuffer/git/OpenMS-fixes-src/cmake-build-debug
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
@jpfeuffer
jpfeuffer / develop.log
Created May 19, 2021 14:41
UpdateCTestConfiguration from :/workspace/OpenMS/build/DartConfiguration.tcl
Parse Config file:/workspace/OpenMS/build/DartConfiguration.tcl
UpdateCTestConfiguration from :/workspace/OpenMS/build/DartConfiguration.tcl
Parse Config file:/workspace/OpenMS/build/DartConfiguration.tcl
Test project /workspace/OpenMS/build
Constructing a list of tests
Done constructing a list of tests
Updating test list for fixtures
Added 0 tests to meet fixture requirements
Checking test dependency graph...
@jpfeuffer
jpfeuffer / out.mzTab
Created March 12, 2021 13:04
MTD mzTab-version 1.0.0
MTD mzTab-mode Summary
MTD mzTab-type Quantification
MTD title ConsensusMap export from OpenMS
MTD description OpenMS export from consensusXML
MTD protein_search_engine_score[1] [MS, MS:1003117, OpenMS:Target-decoy protein q-value, ]
MTD peptide_search_engine_score[1] [MS, MS:1003114, OpenMS:Best PSM Score, ]
MTD psm_search_engine_score[1] [, , MS-GF+ Posterior Error Probability, ]
MTD software[1] [MS, MS:1000752, TOPP software, 2.6.0-pre-develop-2021-02-09]
MTD software[2] [MS, MS:1002203, TOPP ProteinInference, 2.6.0-pre-develop-2021-02-09]
@jpfeuffer
jpfeuffer / mergetest.nf
Created May 5, 2020 17:07
Channel.of( 1, 3, 5, 7 ).into{ ch_branchA; ch_branchB }
process a1 {
input:
val x from ch_branchA
output:
tuple x, file('x.txt') into ch_A1
"""
echo $x > x.txt
@jpfeuffer
jpfeuffer / test.nf
Last active March 26, 2020 16:26
Little nextflow script to parse sdrf
ch_sdrf = Channel.fromPath(params.sdrf, checkIfExists: true)
ch_sdrf.splitCsv(sep:'\t', header: true)
.map{ row-> tuple(file(row.'comment[file uri]'), row.'comment[precursor mass tolerance]') }
.groupTuple()
.subscribe { println it}
@jpfeuffer
jpfeuffer / gist:a5847aca26de0c969ea50f7dd7ef0984
Created December 23, 2019 11:23
foosha
79445708ac44bdbae5ef95322e4b39b2
@jpfeuffer
jpfeuffer / create_trivial_openms_exp_design.sh
Created October 17, 2019 16:37
Creates a trivial experimental design for LFQ use with the OpenMS proteomicsLFQ tool.
#!/usr/bin/python
import sys
import glob
import re
# code to sort in a human readable way
def atoi(text):
return int(text) if text.isdigit() else text
@jpfeuffer
jpfeuffer / Seqantcoffee.ctd
Created July 26, 2019 08:46
Seqan tcoffee ctd
seqan_tcoffee Multiple sequence alignment SeqAn::T-Coffee is a multiple sequence alignment tool. (c) Copyright 2009 by Tobias Rausch
This XML file does not appear to have any style information associated with it. The document tree is shown below.
<tool name="SeqanTcoffee" version="1.13.8 [e165baf]" docurl="http://www.seqan.de" category="Sequence Alignment">
<executableName>seqan_tcoffee</executableName>
<description>Multiple sequence alignment</description>
<manual>
SeqAn::T-Coffee is a multiple sequence alignment tool. (c) Copyright 2009 by Tobias Rausch
</manual>
<manual>...</manual>
<cli>
@jpfeuffer
jpfeuffer / gist:42ba3dbe9b79dc3966c3f7d894762c86
Created January 22, 2019 12:05
unordered_map error String
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\include\xhash(29): error C2440: 'type cast': cannot convert from 'const OpenMS::String' to 'std::size_t' (compiling source file C:\jenkins\ws\openms_user_experimental\openms_test_packaging\c2e226b2\source\src\openms\source\FORMAT\HANDLERS\MascotXMLHandler.cpp) [C:\jenkins\ws\openms_user_experimental\openms_test_packaging\c2e226b2\build\src\openms\OpenMS.vcxproj]
C:\Program Files (x86)\Microsoft Visual Studio 14.0\VC\include\xhash(29): note: No user-defined-conversion operator available that can perform this conversion, or the operator cannot be called (compiling source file C:\jenkins\ws\openms_user_experimental\openms_test_packaging\c2e226b2\source\src\openms\source\FORMAT\HANDLERS\MascotXMLHandler.cpp)
C:\jenkins\ws\openms_user_experimental\openms_test_packaging\c2e226b2\contrib_build\include\boost/functional/hash/extensions.hpp(262): note: see reference to function template instantiation 'size_t stdext::hash_value<T>(const _Kty &)' being compiled