fix installation paths

README.md

@@ -79,9 +79,9 @@ The command uses **--recurse-submodules** to download the submodules. The flag i
 
 ```
 cd install/
-SETENV.sh snakemake_env
+./SETENV.sh snakemake_env
 conda activate snakemake_env
-TESTING.sh
+./TESTING.sh
 ```
 
 ### <a name="usage"></a>Usage and Input
@@ -187,7 +187,7 @@ To only create the folder and config files, please turn off the last six options
 The folder *examples/* includes a structured zip file and a yaml file--the two input formats that Seq2Geno can recognize. The zip file can be used as the input with this command:
 
 ```
-S2G -z examples/example_input.zip\
+S2G -z examples/example_input/seq2geno_input.yml\
  -l examples/example_input_zip.log\
  --outzip g2p
 ```
@@ -197,7 +197,7 @@ is, the zip file) and edit the yaml file to ensure the right paths to
 those example data. After they are ready, please run with this command:
 
 ```
-S2G -f examples/seq2geno_input.yml\
+S2G -f examples/example_input/seq2geno_input.yml\
  -l exapmles/seq2geno_input_yml.log\
  --outzip g2p
 ```
@@ -209,7 +209,7 @@ To include automatic submission to the Geno2Pheno server, just use the flag
 `--to_gp`:
 
 ```
-S2G -f examples/seq2geno_input.yml\
+S2G -f examples/example_input/seq2geno_input.yml\
  -l exapmles/seq2geno_input_yml.log\
  --outzip g2p --to_gp
 ```

denovo/lib/install_perl_mods.sh

@@ -10,6 +10,7 @@ cpanm --force XML::Parser
 cpanm --force Graph
 cpanm --force Graph::Writer::Dot
 cpanm --force File::Find::Rule
+cpanm --force Exception::Class
 #cpanm Bio::Perl
 #cpanm Moose
 #cpanm Log::Log4perl

install/SETENV.sh

@@ -82,9 +82,6 @@ conda activate $core_env_name || source activate $core_env_name
 set_core_env_vars || { echo "Errors in setting up the core environment"; exit; }
 
 # Finalize
-export SEQ2GENO_HOME=$( dirname $( dirname $( realpath ${BASH_SOURCE[0]} ) ) )
-export PATH=$SEQ2GENO_HOME:$SEQ2GENO_HOME/main:$PATH
-
 cat $SEQ2GENO_HOME/main/S2G| sed "s/_core_env/$core_env_name/g" \
 	> $SEQ2GENO_HOME/S2G
 chmod +x $SEQ2GENO_HOME/S2G

main/S2G

@@ -1,7 +1,7 @@
 #!/usr/bin/env bash
 
 # activate the environment
-source _core_env || conda activate _core_env
+source activate _core_env || conda activate _core_env
 if [ $# -eq 0 ];then
 	seq2geno_gui
 else

main/main_gui.py

@@ -264,7 +264,7 @@ def write_yaml(func_dict, config_dict):
                                          initialdir='.')
     if len(yml_f) > 0:
         primary_dict['yml_f'].set(yml_f)
-        with LoadFile(yml_f) as yml_fh:
+        with open(yml_f, 'w') as yml_fh:
             yaml.safe_dump(arg_dict, yml_fh)
         return(yml_f)