Merge pull request #3 from ERGA-consortium/devel

Devel

assembly/galaxy/2.Contigging/README.md

@@ -19,6 +19,4 @@ Load the respective .ga file in Galaxy to run the workflow.
 
 ### Nextdenovo
 
-### NECAT
-
-### Raven
+### Shasta

assembly/snakemake/1.Genome_Profiling/genoplot/README.md

@@ -8,7 +8,7 @@ To run, you will need to create the following conda environment:
 
 or:
 
-`conda create -n genoplots -c conda-forge -c bioconda --list requirements_genoplots.txt`
+`conda create -n genoplots -c conda-forge -c bioconda --file requirements_genoplots.txt`
 
 And edit the file names in the config.yaml file
 

assembly/snakemake/4.Scaffolding/yahs/requirements_yahs.txt

@@ -0,0 +1,50 @@
+# This file may be used to create an environment using:
+# $ conda create --name <env> --file <this file>
+# platform: osx-64
+blas=1.0=openblas
+bwa=0.7.17=h45fc8d7_11
+bzip2=1.0.8=h0d85af4_4
+c-ares=1.19.1=h0dc2134_0
+ca-certificates=2023.05.30=hecd8cb5_0
+click=8.1.4=unix_pyh707e725_0
+coreutils=9.3=hb7f2c08_0
+htslib=1.17=h365c357_2
+krb5=1.20.1=h049b76e_0
+libblas=3.9.0=17_osx64_openblas
+libcblas=3.9.0=17_osx64_openblas
+libcurl=8.1.2=hbee3ae8_0
+libcxx=16.0.6=hd57cbcb_0
+libdeflate=1.18=hac1461d_0
+libedit=3.1.20191231=h0678c8f_2
+libev=4.33=haf1e3a3_1
+libffi=3.4.2=h0d85af4_5
+libgfortran=5.0.0=11_3_0_h97931a8_31
+libgfortran5=12.2.0=he409387_31
+liblapack=3.9.0=17_osx64_openblas
+libnghttp2=1.52.0=he2ab024_0
+libopenblas=0.3.23=openmp_h429af6e_0
+libsqlite=3.42.0=h58db7d2_0
+libssh2=1.11.0=hd019ec5_0
+libzlib=1.2.13=h8a1eda9_5
+llvm-openmp=16.0.6=hff08bdf_0
+lz4-c=1.9.4=hf0c8a7f_0
+ncurses=6.4=hf0c8a7f_0
+numpy=1.23.5=py39h57a7bef_0
+numpy-base=1.23.5=py39hc93c6d9_0
+openssl=3.1.1=h8a1eda9_1
+pairtools=0.3.0=py39h33ca528_6
+pbgzip=2016.08.04=h652314c_4
+perl=5.32.1=3_h0dc2134_perl5
+pip=23.1.2=pyhd8ed1ab_0
+python=3.9.16=h709bd14_0_cpython
+python_abi=3.9=3_cp39
+readline=8.2=h9e318b2_1
+samtools=1.17=h25dfcfb_1
+setuptools=68.0.0=pyhd8ed1ab_0
+tk=8.6.12=h5dbffcc_0
+tzdata=2023c=h71feb2d_0
+wheel=0.40.0=pyhd8ed1ab_0
+xz=5.2.6=h775f41a_0
+yahs=1.2a.2=h45fc8d7_2
+zlib=1.2.13=h8a1eda9_5
+zstd=1.5.2=h829000d_7