From 5fbab058d3fdb5d62efc698e19f9af51057be5d8 Mon Sep 17 00:00:00 2001
From: thkuo <tku16@helmholtz-hzi.de>
Date: Sun, 11 Jul 2021 12:08:15 +0200
Subject: [PATCH] fix installation paths

---
 README.md                       | 10 +++++-----
 denovo/lib/install_perl_mods.sh |  1 +
 install/SETENV.sh               |  3 ---
 main/S2G                        |  2 +-
 main/main_gui.py                |  2 +-
 5 files changed, 8 insertions(+), 10 deletions(-)

diff --git a/README.md b/README.md
index 8e5175c10..593a805cd 100644
--- a/README.md
+++ b/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
 ```
diff --git a/denovo/lib/install_perl_mods.sh b/denovo/lib/install_perl_mods.sh
index 6af256412..9858dd69d 100755
--- a/denovo/lib/install_perl_mods.sh
+++ b/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
diff --git a/install/SETENV.sh b/install/SETENV.sh
index 7159289d8..62b3dfbc7 100755
--- a/install/SETENV.sh
+++ b/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
diff --git a/main/S2G b/main/S2G
index c26052575..12d3c5b5c 100644
--- a/main/S2G
+++ b/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
diff --git a/main/main_gui.py b/main/main_gui.py
index 3e1778f9f..3cbec22a9 100755
--- a/main/main_gui.py
+++ b/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)