diff --git a/.github/auto_interact.exp b/.github/auto_interact.exp index 0293789..ab4dd96 100644 --- a/.github/auto_interact.exp +++ b/.github/auto_interact.exp @@ -25,22 +25,22 @@ expect "Do you want to modify the CPU number? \[y/N\]: " send "N\r" ############################ 2. assign execute permissions ############################# -expect "\n2. Would you like to assign execute permissions to all users for bash and perl files? \[Y/n\]: " +expect "2. Would you like to assign execute permissions to all users for bash and perl files? \[Y/n\]: " send "Y\r" ############################# 3. download homotypic data ############################## -expect "\n3. Would you like to download data of homotypic motif hits? \[y/N\]: " +expect "3. Would you like to download data of homotypic motif hits? \[y/N\]: " send "N\r" ################################## 4. compile binary ################################# -expect "\n4. Would you like to compile binaries? \[y/N\]:" +expect "4. Would you like to compile binaries? \[y/N\]:" send "y\r" ############################# 5. install R packages ############################## -expect "\n6. Would you like to install python packages? \[y/N\]: " +expect "5. Would you like to install R packages? [y/N]: " send "y\r" diff --git a/deploy_one_bash.sh b/deploy_one_bash.sh index 28f9721..54a95ae 100644 --- a/deploy_one_bash.sh +++ b/deploy_one_bash.sh @@ -256,8 +256,8 @@ done ############################ 2. assign execute permissions ############################# - -print_green_no_br "\n2. Would you like to assign execute permissions to all users for bash and perl files? [Y/n]: " +echo "" +print_green_no_br "2. Would you like to assign execute permissions to all users for bash and perl files? [Y/n]: " read -p "" answer answer=${answer:-Y} # Default to 'Y' if no input provided @@ -270,9 +270,6 @@ else fi - - - ############################# 3. download homotypic data ############################## current_dir=$(pwd) @@ -280,12 +277,14 @@ current_dir=$(pwd) data_path="${current_dir}/data/indexing" # 询问用户是否开始下载 -print_green "\n3. Would you like to download data of homotypic motif hits? [y/N]: " -print_orange_no_br "Data path: $data_path" +echo "" +print_green_no_br "3. Would you like to download data of homotypic motif hits? [y/N]: " read -p "" answer answer=${answer:-N} # Default to 'N' if no input provided +print_orange "Data path: $data_path" + urls=( "http://pmet.online:84/result/Arabidopsis_thaliana.tar.gz" "http://pmet.online:84/result/Brachypodium_distachyon.tar.gz" @@ -354,8 +353,8 @@ fi ################################## 4. compile binary ################################# - -print_green_no_br "\n4. Would you like to compile binaries? [y/N]:" +echo "" +print_green_no_br "4. Would you like to compile binaries? [y/N]:" read -p " " answer answer=${answer:-N} # Default to 'N' if no input provided @@ -459,7 +458,8 @@ chmod a+x PMETdev/scripts/pmet chmod a+x PMETdev/scripts/fimo ############################# 5. install R packages ############################## -print_green_no_br "\n5. Would you like to install R packages? [y/N]: " +echo "" +print_green_no_br "5. Would you like to install R packages? [y/N]: " # read -p "Would you like to install R packages? [y/N]: " answer read -p " " answer answer=${answer:-N} # Default to 'N' if no input provided @@ -474,7 +474,8 @@ fi ############################# 6. install python packages ############################## -print_green_no_br "\n6. Would you like to install python packages? [y/N]: " +echo "" +print_green_no_br "6. Would you like to install python packages? [y/N]: " read -p " " answer answer=${answer:-N} # Default to 'N' if no input provided @@ -491,7 +492,8 @@ fi ################################ 7. check needed tools ################################# -print_green "\n7. Checking the existence of GNU Parallel, bedtools, samtools and MEME Suite " +echo "" +print_green "7. Checking the existence of GNU Parallel, bedtools, samtools and MEME Suite " # List of tools to check tools=("parallel" "bedtools" "samtools" "fimo")