rename workpackage2 to goldrush-path

bcgsc · May 20, 2022 · 1ffe000 · 1ffe000
1 parent 1d6161c
commit 1ffe000
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Showing 24 changed files with 7 additions and 7 deletions.
diff --git a/bin/goldrush b/bin/goldrush
@@ -178,14 +178,14 @@ wp2-tigmint-ntLink: ntLink1 $(ntlink_targets) ntLink_softlink
 workpackage2: $(p2)_golden_path_1.fq
 
 $(p2)_golden_path_1.fq: $(p1)_golden_path_all.fq 
-	$(time) workpackage2  -k $(k) -w $(w) -t $(tile) -u $(u) -a $(a) -l $(l) -o $(o) -p $(p2) -i $(p1)_golden_path_all.fq -h $(h) -j $(j) -P $(P) -x$(x) -s $(s) -m 0 
+	$(time) goldrush-path  -k $(k) -w $(w) -t $(tile) -u $(u) -a $(a) -l $(l) -o $(o) -p $(p2) -i $(p1)_golden_path_all.fq -h $(h) -j $(j) -P $(P) -x$(x) -s $(s) -m 0 
 	echo "Done WP2! Golden path can be found in: $@"
 
 $(p1)_golden_path_all.fq: $(p1)_golden_path_$(M).fq
 	cat $(p1)_golden_path_*.fq > $(p1)_golden_path_all.fq
 
 $(p1)_golden_path_$(M).fq: $(long_reads)
-	$(time) workpackage2  -k $(k) -w $(w) -t $(tile) -u $(u) -a $(a) -l $(l) -o $(o) -p $(p1) -i $(long_reads)  -h $(h) -j $(j) -x$(x) -P $(P) -s $(s) -T $(T) -r $(r) --new_temp_mode -M $(M) -m $(m)
+	$(time) goldrush-path  -k $(k) -w $(w) -t $(tile) -u $(u) -a $(a) -l $(l) -o $(o) -p $(p1) -i $(long_reads)  -h $(h) -j $(j) -x$(x) -P $(P) -s $(s) -T $(T) -r $(r) --new_temp_mode -M $(M) -m $(m)
 
 
 # Run racon 

diff --git a/...kage2/Common/.deps/libcommon_a-Options.Po → ..._path/Common/.deps/libcommon_a-Options.Po b/...kage2/Common/.deps/libcommon_a-Options.Po → ..._path/Common/.deps/libcommon_a-Options.Po
diff --git a/workpackage2/Common/IOUtil.h → goldrush_path/Common/IOUtil.h b/workpackage2/Common/IOUtil.h → goldrush_path/Common/IOUtil.h
diff --git a/workpackage2/Common/Makefile.am → goldrush_path/Common/Makefile.am b/workpackage2/Common/Makefile.am → goldrush_path/Common/Makefile.am
diff --git a/workpackage2/Common/Options.cpp → goldrush_path/Common/Options.cpp b/workpackage2/Common/Options.cpp → goldrush_path/Common/Options.cpp
diff --git a/workpackage2/Common/Options.h → goldrush_path/Common/Options.h b/workpackage2/Common/Options.h → goldrush_path/Common/Options.h
diff --git a/workpackage2/MIBFConstructSupport.hpp → goldrush_path/MIBFConstructSupport.hpp b/workpackage2/MIBFConstructSupport.hpp → goldrush_path/MIBFConstructSupport.hpp
diff --git a/workpackage2/MIBloomFilter.hpp → goldrush_path/MIBloomFilter.hpp b/workpackage2/MIBloomFilter.hpp → goldrush_path/MIBloomFilter.hpp
diff --git a/workpackage2/Options.cpp → goldrush_path/Options.cpp b/workpackage2/Options.cpp → goldrush_path/Options.cpp
diff --git a/workpackage2/Options.h → goldrush_path/Options.h b/workpackage2/Options.h → goldrush_path/Options.h
diff --git a/workpackage2/calc_phred_average.cpp → goldrush_path/calc_phred_average.cpp b/workpackage2/calc_phred_average.cpp → goldrush_path/calc_phred_average.cpp
diff --git a/workpackage2/calc_phred_average.hpp → goldrush_path/calc_phred_average.hpp b/workpackage2/calc_phred_average.hpp → goldrush_path/calc_phred_average.hpp
diff --git a/workpackage2/workpackage2.cpp → goldrush_path/goldrush_path.cpp b/workpackage2/workpackage2.cpp → goldrush_path/goldrush_path.cpp
diff --git a/workpackage2/meson.build → goldrush_path/meson.build b/workpackage2/meson.build → goldrush_path/meson.build
@@ -1,12 +1,12 @@
-src_files = [ 'workpackage2.cpp', 'Options.cpp', 'read_hashing.cpp', 'opt.cpp', 'spaced_seeds.cpp', 'calc_phred_average.cpp' ]
+src_files = [ 'goldrush_path.cpp', 'Options.cpp', 'read_hashing.cpp', 'opt.cpp', 'spaced_seeds.cpp', 'calc_phred_average.cpp' ]
 deps = [ btllib_dep, threads_dep, openmp_dep, tcmalloc_dep, divsufsort_dep, divsufsort64_dep, sdsl_dep ]
 inc_dirs = [ 'Common' ]
 link_args = [ '-ltcmalloc', '-lsdsl', '-ldivsufsort', '-ldivsufsort64' ]
 
-executable('workpackage2',
+executable('goldrush-path',
     src_files,
     dependencies : deps,
     include_directories : inc_dirs,
     link_args : link_args,
     install : true
-)
+)
diff --git a/workpackage2/multiLensfrHashIterator.hpp → goldrush_path/multiLensfrHashIterator.hpp b/workpackage2/multiLensfrHashIterator.hpp → goldrush_path/multiLensfrHashIterator.hpp
diff --git a/workpackage2/ntcard.hpp → goldrush_path/ntcard.hpp b/workpackage2/ntcard.hpp → goldrush_path/ntcard.hpp
diff --git a/workpackage2/nthash.hpp → goldrush_path/nthash.hpp b/workpackage2/nthash.hpp → goldrush_path/nthash.hpp
diff --git a/workpackage2/opt.cpp → goldrush_path/opt.cpp b/workpackage2/opt.cpp → goldrush_path/opt.cpp
diff --git a/workpackage2/opt.hpp → goldrush_path/opt.hpp b/workpackage2/opt.hpp → goldrush_path/opt.hpp
diff --git a/workpackage2/read_hashing.cpp → goldrush_path/read_hashing.cpp b/workpackage2/read_hashing.cpp → goldrush_path/read_hashing.cpp
diff --git a/workpackage2/read_hashing.hpp → goldrush_path/read_hashing.hpp b/workpackage2/read_hashing.hpp → goldrush_path/read_hashing.hpp
diff --git a/workpackage2/spaced_seeds.cpp → goldrush_path/spaced_seeds.cpp b/workpackage2/spaced_seeds.cpp → goldrush_path/spaced_seeds.cpp
diff --git a/workpackage2/spaced_seeds.hpp → goldrush_path/spaced_seeds.hpp b/workpackage2/spaced_seeds.hpp → goldrush_path/spaced_seeds.hpp
diff --git a/meson.build b/meson.build
@@ -14,11 +14,11 @@ divsufsort_dep = compiler.find_library('divsufsort')
 divsufsort64_dep = compiler.find_library('divsufsort64')
 sdsl_dep = compiler.find_library('sdsl')
 
-subdir('workpackage2')
+subdir('goldrush_path')
 
 rootpath = meson.source_root()
 
 clang_format = find_program('clang-format', required : false)
 if clang_format.found()
   run_target('format', command: join_paths(rootpath, 'scripts/format'))
-endif
+endif