Merge pull request #103 from rseng/update/analysis-2024-01-10

Update from update/analysis-2024-01-10
rseng · Jan 10, 2024 · d5ea910 · d5ea910
2 parents ed5ffd9 + 1e1a207
commit d5ea910
Show file tree

Hide file tree

Showing 7 changed files with 208 additions and 154 deletions.
diff --git a/_repos/github/ByrumLab/proteoDA/DESCRIPTION b/_repos/github/ByrumLab/proteoDA/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: proteoDA
 Title: Streamlined Differential Abundance Analysis of Proteomic Data
-Version: 0.0.0.9002
+Version: 1.0.1
 Authors@R: 
  c(
  person(given = "Timothy", family = "Thurman", email = "[email protected]", role = c("aut", "cre")),
@@ -37,6 +37,7 @@ Depends:
 Suggests:
  grDevices,
  ggrastr,
+ tibble,
  testthat (>= 3.0.0)
 Config/testthat/edition: 3
 Encoding: UTF-8

diff --git a/_repos/github/CRPropa/CRPropa3/CMakeLists.txt b/_repos/github/CRPropa/CRPropa3/CMakeLists.txt
@@ -245,17 +245,6 @@ if(ENABLE_QUIMBY)
  endif(QUIMBY_FOUND)
 endif(ENABLE_QUIMBY)
 
-# SAGA (optinal for AMR grids)
-find_package(SAGA)
-if(SAGA_FOUND)
- list(APPEND CRPROPA_EXTRA_INCLUDES ${SAGA_INCLUDE_DIR})
- list(APPEND CRPROPA_EXTRA_LIBRARIES ${SAGA_LIBRARY})
- add_definitions (-DCRPROPA_HAVE_SAGA)
- list(APPEND CRPROPA_SWIG_DEFINES -DCRPROPA_HAVE_SAGA)
- list(APPEND SWIG_INCLUDE_DIRECTORIES ${SAGA_INCLUDE_DIR}/../python)
- list(APPEND SWIG_INCLUDE_DIRECTORIES ${SAGA_INCLUDE_DIR})
-endif(SAGA_FOUND)
-
 # muparser (optional for generic source spectra)
 find_package(muParser)
 if(MUPARSER_FOUND)

diff --git a/_repos/github/Griffan/VerifyBamID/CMakeLists.txt b/_repos/github/Griffan/VerifyBamID/CMakeLists.txt
@@ -65,7 +65,7 @@ target_link_libraries(VerifyBamID statgen Vcf ${HTS_LIBRARIES} samtools ${ZLIB}
 enable_testing()
 add_test(NAME myTest1
  WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
- COMMAND VerifyBamID --DisableSanityCheck --BamFile resource/test/test.bam --SVDPrefix resource/test/hapmap_3.3.b37.dat --Reference resource/test/chr20.fa.gz)
+ COMMAND VerifyBamID --DisableSanityCheck --BamFile resource/test/test.bam --SVDPrefix resource/test/hapmap_3.3.b37.dat --Reference resource/test/chr20.fa.gz --NumPC 2)
 #add_test( NAME myTest2
 # WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
 # COMMAND sh ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/run.plot.sh -i ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap_3.3.b37.dat.V -o ${CMAKE_CURRENT_SOURCE_DIR}/resource/test/hapmap -r 1000g -g grey)