Merge pull request #156 from DennisSchmitz/p1.0.1

Patch 1.0.01
DennisSchmitz · Jul 3, 2020 · b6cfbf1 · b6cfbf1
2 parents b6fe4bf + 62167b5
commit b6cfbf1
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Showing 23 changed files with 18 additions and 14 deletions.
diff --git a/bin/envs/Jovian_master_environment.yaml b/bin/envs/Jovian_master_environment.yaml
@@ -26,5 +26,6 @@ dependencies:
   - seqkit==0.12.1
   - pv==1.6.6
   - pip==19.2.3
+  - bc
   - pip:
     - PyYAML==5.3.1
diff --git a/bin/includes/Archive b/bin/includes/Archive
diff --git a/bin/includes/Clean b/bin/includes/Clean
diff --git a/bin/includes/Config_jupyter b/bin/includes/Config_jupyter
diff --git a/bin/includes/Databases b/bin/includes/Databases
diff --git a/bin/includes/Databases_installer b/bin/includes/Databases_installer
diff --git a/bin/includes/Install_conda_envs b/bin/includes/Install_conda_envs
diff --git a/bin/includes/Install_jovian-master b/bin/includes/Install_jovian-master
diff --git a/bin/includes/Install_miniconda b/bin/includes/Install_miniconda
diff --git a/bin/includes/Make_ncbirc b/bin/includes/Make_ncbirc
diff --git a/bin/includes/Make_samplesheet b/bin/includes/Make_samplesheet
diff --git a/bin/includes/Mode b/bin/includes/Mode
diff --git a/bin/includes/Pre_install_checker b/bin/includes/Pre_install_checker
diff --git a/bin/includes/Preflight_check_databases b/bin/includes/Preflight_check_databases
diff --git a/bin/includes/Preflight_readlength-counter b/bin/includes/Preflight_readlength-counter
diff --git a/bin/includes/Rebuild_archive b/bin/includes/Rebuild_archive
@@ -13,22 +13,22 @@ minispacer
 line
 minispacer
 
-eval $(parse_yaml profile/variables.yaml "vars_")
+eval $(parse_yaml config/variables.yaml "vars_")
 oldhostname="$vars_Server_host_hostname"
 newhostname="http://${HOSTNAME}"
 
 
 ###### Modifying the HTML index file for IGVjs
-if [ -e results/IGVjs_index.html ]; then
+if [ -e results/igv.html ]; then
     echo -e "Modifying IGVjs index file..."
-    sed -i -e "s@${oldhostname}@${newhostname}@g" "results/IGVjs_index.html"
+    sed -i -e "s@${oldhostname}@${newhostname}@g" "results/igv.html"
 fi
 
 
-if [ -e profile/variables.yaml ]; then
+if [ -e config/variables.yaml ]; then
     echo -e "Resetting some of the variables..."
-    sed '3,4d' -i profile/variables.yaml
-    echo -e "Server_host:\n    hostname: http://${HOSTNAME}" >> profile/variables.yaml
+    sed '3,4d' -i config/variables.yaml
+    echo -e "Server_host:\n    hostname: http://${HOSTNAME}" >> config/variables.yaml
 fi
 
 minispacer
@@ -39,7 +39,7 @@ minispacer
 
 if [ ! -h /tmp/etc/nginx/default-site/$vars_Jovian_run_identifier ]; then
     echo -e "Setting symlink..."
-    bin/set_symlink.sh
+    bin/scripts/set_symlink.sh
 else
     echo "Symlink has already been set"
 fi

diff --git a/bin/includes/Start_jupyter b/bin/includes/Start_jupyter
diff --git a/bin/includes/Typingtool_check b/bin/includes/Typingtool_check
diff --git a/bin/includes/Userconfig_CM b/bin/includes/Userconfig_CM
diff --git a/bin/includes/Userconfig_DB b/bin/includes/Userconfig_DB
diff --git a/bin/includes/Version b/bin/includes/Version
diff --git a/bin/includes/functions b/bin/includes/functions
@@ -39,9 +39,6 @@ installer_intro() {
     echo -e "Welcome to the interactive installation process of Jovian"
     echo -e "You are seeing this because one or multiple dependencies of Jovian are missing on your system."
     echo -e "You are using Jovian $VERSION"
-    spacer
-    echo -e "Please keep in mind that this pipeline is still a work-in-progress"
-    echo -e "It is expected that several portions are unstable until release 1.0.0"
     line
     spacer
 }
@@ -73,8 +70,6 @@ ready_for_start() {
     line
     echo -e "All pre-flight checks of Jovian have been completed"
     echo -e "You are using Jovian version ${VERSION}"
-    echo -e "Please keep in mind that this pipeline is still a work-in-progress"
-    echo -e "It is expected that several portions are unstable until release 1.0.0"
     line
     spacer
 }

diff --git a/bin/includes/selfupdate b/bin/includes/selfupdate
@@ -1,6 +1,8 @@
 #!/bin/bash
 # shellcheck disable=SC1091
 
+conda deactivate
+
 if [ "${1}" == "master" ]; then
 
 	echo -e "Updating Jovian will delete \e[1m all local changes\e[0m that you've made."
@@ -31,7 +33,10 @@ if [ "${1}" == "master" ]; then
 	git checkout master
 	git fetch origin --tags "${latestrelease}"
 	git reset --hard FETCH_HEAD
-	conda env update --file "${PATH_JOVIAN_MASTER_YAML}"
+	conda remove --name "${MASTER_NAME}" --all -y
+	conda remove --name "${HELPER_NAME}" --all -y
+	bash bin/includes/Install_jovian-master
+	conda env create -f ${PATH_JOVIAN_HELPER_YAML}
 
 	echo -e "DONE"
 
@@ -64,7 +69,10 @@ else
 	git checkout master	
 	git fetch origin --tags "${1}"
 	git reset --hard FETCH_HEAD
-	conda env update --file "${PATH_JOVIAN_MASTER_YAML}"
+	conda remove --name "${MASTER_NAME}" --all -y
+	conda remove --name "${HELPER_NAME}" --all -y
+	bash bin/includes/Install_jovian-master
+	conda env create -f ${PATH_JOVIAN_HELPER_YAML}
 
 	echo -e "DONE"
 fi