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Support for tmt-18 and other improvements #82

Merged
merged 22 commits into from
May 23, 2024
Merged

Support for tmt-18 and other improvements #82

merged 22 commits into from
May 23, 2024
+966 −408

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biodavidjm
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  • Add support for tmt-18
    • Adding tmt-18 config templates for msgfplus
    • Add new MASIC config file
  • Software updates (dockerfiles updated)
    • Masic
    • msgfplus
    • phpr
    • mzid2tsv
    • ppmerror (this is not used for now due to an error that will have to be debugged, i.e., the template has not yet been updated)
  • create_study_design.R: several improvements
  • New msgfplus config files that will be relevant for the next assay: OX (ReDox)

@biodavidjm
update create_study_design: add 1 to reference.txt if no Ref is present
ad81a75 
#80
@biodavidjm
update create_study_design: add 1 to reference.txt if no Ref is prese…
9ca4279 
…nt, improved version
@biodavidjm
update create_study_design: minor adjustment
1def419
@biodavidjm
Update create_study_design.R: several improvements
1003f08 
- MeasurementName is change for the reference channel based on ReporterAlias, i.e., MeasurementName will be NA only if ReporterAlias is Reference (ref)
- Other adjustments and cleanings
@biodavidjm
fix: create study design: read vial_metadata
9fcc8a9
@biodavidjm
create_study_design: refactor the creation of MeasurementName
30655d7 
dplyr is giving errors, using base r
@biodavidjm
create_study_design: multiple updates
41d8603 
#81
@biodavidjm
update create_config_msgfplus: add tmt18
06091fe 
#81
@biodavidjm
Create config-msgfplus-pr-tmt18.json
ed65418 
#81
@biodavidjm
Update TMT16_10ppm_ReporterTol0.003Da_2019-10-07.xml
809649f
@biodavidjm
Update Mass_Correction_Tags.txt
e3b64e5
@biodavidjm
Create TMT18_10ppm_ReporterTol0.003Da_2021-01-24.xml
2ad9dfc
@biodavidjm
Update copy_pipeline_results.py
50730f7 
minor update
@biodavidjm
Update MASIC to support tmt-18
d243ce3
@biodavidjm
Update Dockerfile.msgfplus
a078a1e
@biodavidjm
Update Dockerfile.mzid2tsv
c390597
@biodavidjm
Update Dockerfile.phrp
6e2064e
@biodavidjm
Update Dockerfile.ppmerror
f8c392f
@biodavidjm
Update input templates msgfplus with new software versions
5396bdd
@biodavidjm
New version of phrp, debian based, and back to previous prot-ppmerror…
7fb0275 
… version
@biodavidjm
Config file for redox
d71f2b9
@biodavidjm
Add msgplus templates for tmt-18 PTMs
db9e621
@biodavidjm biodavidjm requested a review from mihirsamdarshi May 23, 2024 05:31
@biodavidjm biodavidjm merged commit f72164c into develop May 23, 2024
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@mihirsamdarshi mihirsamdarshi

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@biodavidjm @mihirsamdarshi