Updated TIPP (#52968)

* Committer: Anupam Gautam <[email protected]> TIPP_plastid is a User-Friendly Tool for De Novo Assembly of Organellar Genomes with HiFi Data * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/tipp/build.sh Co-authored-by: Martin Grigorov <[email protected]> * Update recipes/tipp/meta.yaml Co-authored-by: Martin Grigorov <[email protected]> * Committer: Anupam Gautam <[email protected]> suggestion incorporated * Committer: Anupam Gautam <[email protected]> updated meta and build. * GenEra conda recipes * removed genera files * adjusted python * update * update * Update meta.yaml * update * update * Update meta.yaml * Update meta.yaml * updated tipp * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * Update meta.yaml * updated tipp --------- Co-authored-by: Anupam Gautam <[email protected]> Co-authored-by: Martin Grigorov <[email protected]> Co-authored-by: richard-burhans <[email protected]> Co-authored-by: Anupam Gautam <[email protected]>
bioconda · Dec 23, 2024 · 443f35a · 443f35a
1 parent 956c724
commit 443f35a
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Showing 2 changed files with 11 additions and 10 deletions.
diff --git a/recipes/tipp/build.sh b/recipes/tipp/build.sh
@@ -25,10 +25,10 @@ make CC=${CC} CFLAGS="${CFLAGS}" LDFLAGS="${LDFLAGS}" all -j "${CPU_COUNT}"
 cd ..
 
 # Compile readskmercount as an object first if it doesn't have a main
-${CXX}  -c readskmercount.opt.cpp -I./kmc3
+${CXX}  -c readskmercount.opt.parameter.cpp -I./kmc3
 
 # Then link it to create the executable
-${CXX}  -o readskmercount readskmercount.opt.o -L./kmc3/bin -lkmc_core -pthread
+${CXX}  -o readskmercount readskmercount.opt.parameter.o -L./kmc3/bin -lkmc_core -pthread
 
 # Copy everything to the Conda environments bin directory to ensure they're accessible
 echo "Copying binaries to PREFIX..."
@@ -46,7 +46,7 @@ for file in *.r; do
 done
 
 
-cp graph.plot.r readskmercount TIPP.pl TIPP_polish.pl html2repeatbed.pl MSA.plot.r TIPP_plastid.pl TIPP_telomere_backup.pl readskmercount.cpp telomeres.visulization.r TIPP_plastid.v2.1.pl TIPP_telomere.pl TIPPo.v2.3.pl TIPPo.v2.2.pl "$PREFIX/bin/" || { echo "Failed to copy specific binaries to PREFIX"; exit 1; }
+cp graph.plot.r readskmercount TIPP.pl TIPP_polish.pl html2repeatbed.pl MSA.plot.r TIPP_plastid.pl TIPP_telomere_backup.pl readskmercount.cpp telomeres.visulization.r asm_defaults.cfg asm_hifi.cfg TIPP_plastid.v2.1.pl TIPP_telomere.pl TIPPo.v2.4.pl TIPPo.v2.3.pl TIPPo.v2.2.pl "$PREFIX/bin/" || { echo "Failed to copy specific binaries to PREFIX"; exit 1; }
 cp -r kmc3/bin $PREFIX/bin/kmc3/
 cp seqtk/seqtk $PREFIX/bin/seqtk/
 

diff --git a/recipes/tipp/meta.yaml b/recipes/tipp/meta.yaml
@@ -1,11 +1,11 @@
 package:
   name: tipp
-  version: "1.2.0"
+  version: "1.3.0"
 
 source:
   git_url: https://github.com/Wenfei-Xian/TIPP.git
-  git_tag: v1.2.0
-  sha256: fd3004af512956ab8eba076e7fc19778cf8daca36a11c27a5fcce3991412108b
+  git_tag: v1.3.0
+  sha256: 58f2bf8de8956b082ebc4438fabe03d4d764ad9c6f221c68d4d244347e00ce3b
 
 build:
   number: 0
@@ -18,14 +18,15 @@ requirements:
     - {{ compiler('cxx') }}  # For compiling C++ code
     - make
     - kmc
+    - zlib
     - libzlib >=1.2.13,<1.3.0
   host:
-    - python >=3.8,<3.9
-    - zlib
+    - python >=3.8.0,<3.9
+    - zlib >=1.2.13,<1.3.0
     - perl
     - libzlib >=1.2.13,<1.3.0
   run:
-    - python >=3.8,<3.9
+    - python >=3.8.0,<3.9
     - libxcrypt
     - tiara
     - graphaligner =1.0.17
@@ -41,12 +42,12 @@ requirements:
     - trf =4.09.1
     - zlib
     - perl
-
 test:
   commands:
     - TIPP_plastid.v2.1.pl -h
     - TIPP_telomere.pl -h
     - TIPPo.v2.3.pl -h
+    - TIPPo.v2.4.pl -h
 
 about:
   home: https://github.com/Wenfei-Xian/TIPP