Makefile issue for smartie-sv

[awaisfarooq724]

I am unable to install smartie-SV because the system runs into a Makefile error. I will write below the error that is causing this error, I have tried contacting the smartie-SV team but they are not responding. Is there anyway you can help me to get it installed so that I can push forward my analysis.
./Makefile: line 1: .PHONY:: command not found
./Makefile: line 3: all:: command not found
./Makefile: line 5: bin/blasr:: No such file or directory
./Makefile: line 6: MAKE: command not found
./Makefile: line 8: bin/printGaps:: No such file or directory
./Makefile: line 9: cd: src/print_gaps: No such file or directory
./Makefile: line 11: src/htslib/libhts.a:: No such file or directory
./Makefile: line 12: cd: src/htslib: No such file or directory
./Makefile: line 14: bin:: command not found
./Makefile: line 17: clean:: command not found

As it appears, there is an issue with .PHONY

[caixu0518]

Sorry, I dont know how to fix this problem. But i can share my 'smartie-sv' file with you. I have installed it successfully in my server. I hope this compiled program can be run directly on your server.

transfer link: https://cowtransfer.com/s/e31c7bedbdbe4a or access [ cowtransfer.com ] and input extract code: t824xf to download;

Best,
Xu

[awaisfarooq724]

thanks for responding to the last issue and I was able to resolve this one using directly on linux server. Now, I have encounrtered another issue...
perl 01.Reference_Nonreference_TEinsertion.pl -query query.info.txt -ref reference.info.lst -TElib EDTA.TElib.fa -bin /home/baicai/smartie-sv/bin -script /home/data1/baicai/AWAIS/dependencies/ITIPs-main/scripts/
Wed Jul 27 16:30:56 2022: COMMAND: perl /home/data1/baicai/AWAIS/dependencies/ITIPs-main/scripts//Run_smartie-sv.pl 2127 ref.fa ref /home/baicai/smartie-sv/bin
Cwd.c: loadable library and perl binaries are mismatched (got handshake key 0xde00080, needed 0xed00080)
failed: perl /home/data1/baicai/AWAIS/dependencies/ITIPs-main/scripts//Run_smartie-sv.pl 2127 ref.fa ref /home/baicai/smartie-sv/bin
can you please assist me, how can I resolve this one?

[awaisfarooq724]

I have used the link that you have just sent and downloaded that but it is still causing errors as follows
(blasrenv) baicai@bioinformatics-07:/home/data1/baicai/AWAIS/dependencies/ITIPs-main$ perl 01.Reference_Nonreference_TEinsertion.pl -query query.info.txt -ref reference.info.lst -TElib EDTA.TElib.fa -bin /home/data1/baicai/AWAIS/dependencies/smartie-sv/bin -script /home/data1/baicai/AWAIS/dependencies/ITIPs-main/scripts/
Fri Aug 12 18:13:41 2022: COMMAND: perl /home/data1/baicai/AWAIS/dependencies/ITIPs-main/scripts//Run_smartie-sv.pl 2127 ref.fa ref /home/data1/baicai/AWAIS/dependencies/smartie-sv/bin
Use of uninitialized value $smartie_sv in concatenation (.) or string at /home/data1/baicai/AWAIS/dependencies/ITIPs-main/scripts//Run_smartie-sv.pl line 21.
Error: cannot find: /sawriter
failed: perl /home/data1/baicai/AWAIS/dependencies/ITIPs-main/scripts//Run_smartie-sv.pl 2127 ref.fa ref /home/data1/baicai/AWAIS/dependencies/smartie-sv/bin
please help me sort out this error