After running setup.py, we didn't find install.sh to proceed.

minn333 commented 2 years ago

Dear author, As the title, we followed your instruction to install MutpredSuite, however, we didn't find install.sh. Could you kindly solve the problem. Thanks a lot!

trberg commented 2 years ago

Hi @minn333, I see the install.sh file in the github repo, did the file not make to your local environment when you cloned the repo?

minn333 commented 2 years ago

Dear Bergquist I will refer your mail to system administrator, thanks for your reply. With best wishes,Demin Duan 從 Windows 的郵件傳送寄件者: Timothy Bergquist傳送時間: 2022年6月2日上午 03:10收件者: NCBI-Hackathons/MutPredMerge副本: minn333; Mention主旨: Re: [NCBI-Hackathons/MutPredMerge] After running setup.py, we didn't find install.sh to proceed. (Issue #2) Hi @minn333, I see the install.sh file in the github repo, did the file not make to your local environment when you cloned the repo?—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>

trberg commented 2 years ago

If you're having issues, you can create a bash file called install.sh, and paste the following code into the file.

#!/bin/sh
# script for execution of deployed applications
#
#Installs the needed packages and programs for MutPredMerge

while true; do
    read -p "The installation of the MutPred Suite takes 90 Gb? Do you wish to continue? " yn
    case $yn in
        [Yy]* ) 
            # download and unzip mutpred2
            wget --directory-prefix=tools/ http://mutpred.mutdb.org/mutpred2.0_linux_x86_64.tar.gz;
            tar -xvzf tools/mutpred2.0_linux_x86_64.tar.gz;
            rm tools/mutpred2.0_linux_x86_64.tar.gz;
            printf "[NCBI]\nDATA=$(pwd)/tools/mutpred2.0/blast-2.2.18/data/" > tools/mutpred2.0/.ncbirc;
            source tools/mutpred2.0/.ncbirc;
            echo "ignore this error, all is fine";

            #download and unzip mutpred LOF
            wget --directory-prefix=tools/ http://mutpredlof.cs.indiana.edu/MutPredLOF_compiled.tar.gz;
            tar -xvzf tools/MutPredLOF_compiled.tar.gz;
            rm tools/MutPredLOF_compiled.tar.gz;
            cp -r tools/mutpred2.0/v91/ tools/MutPredLOF/;

            #download and unzip mutpred indels
            wget --directory-prefix=tools/ http://mutpredindel.cs.indiana.edu/MutPredIndel_compiled.tar.gz;
            tar -xvzf tools/MutPredIndel_compiled.tar.gz;
            rm tools/MutPredIndel_compiled.tar.gz;
            cp -r tools/mutpred2.0/v91/ tools/MutPredIndel_compiled/;
            break;;
        [Nn]* ) exit;;
        * ) echo "Please answer yes or no.";;
    esac
done

Hope this helps!

minn333 commented 2 years ago

Dear Bergquist Thanks for your kindly help. I will refer to system administrator. With best wishes,Demin, Duan 從 Windows 的郵件傳送寄件者: Timothy Bergquist傳送時間: 2022年6月3日上午 01:12收件者: NCBI-Hackathons/MutPredMerge副本: minn333; Mention主旨: Re: [NCBI-Hackathons/MutPredMerge] After running setup.py, we didn't find install.sh to proceed. (Issue #2) If you're having issues, you can create a bash file called install.sh, and paste the following code into the file.#!/bin/sh# script for execution of deployed applications##Installs the needed packages and programs for MutPredMerge while true; do read -p "The installation of the MutPred Suite takes 90 Gb? Do you wish to continue? " yn case $yn in [Yy]* ) # download and unzip mutpred2 wget --directory-prefix=tools/ http://mutpred.mutdb.org/mutpred2.0_linux_x86_64.tar.gz; tar -xvzf tools/mutpred2.0_linux_x86_64.tar.gz; rm tools/mutpred2.0_linux_x86_64.tar.gz; printf "[NCBI]\nDATA=$(pwd)/tools/mutpred2.0/blast-2.2.18/data/" > tools/mutpred2.0/.ncbirc; source tools/mutpred2.0/.ncbirc; echo "ignore this error, all is fine"; #download and unzip mutpred LOF wget --directory-prefix=tools/ http://mutpredlof.cs.indiana.edu/MutPredLOF_compiled.tar.gz; tar -xvzf tools/MutPredLOF_compiled.tar.gz; rm tools/MutPredLOF_compiled.tar.gz; cp -r tools/mutpred2.0/v91/ tools/MutPredLOF/; #download and unzip mutpred indels wget --directory-prefix=tools/ http://mutpredindel.cs.indiana.edu/MutPredIndel_compiled.tar.gz; tar -xvzf tools/MutPredIndel_compiled.tar.gz; rm tools/MutPredIndel_compiled.tar.gz; cp -r tools/mutpred2.0/v91/ tools/MutPredIndel_compiled/; break;; [Nn]* ) exit;; * ) echo "Please answer yes or no.";; esacdoneHope this helps!—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you were mentioned.Message ID: ***@***.***>

NCBI-Hackathons / MutPredMerge

After running setup.py, we didn't find install.sh to proceed. #2