Cannot use SRA data access in HISAT2

[atonidas]

everytime I try to run this command, i got this error :

$ hisat2 -p 8 --dta -x chrX_data/indexes/chrX_tran --sra-acc ERR188245 –S ERR188245_chrX.sam
hisat2-align-s: unrecognized option '--sra-acc'

so that I follow this instruction and download ngs-sdk.1.3.0-linux.tar.gz

"For the support of SRA data access in HISAT2, please download and install the NCBI-NGS toolkit."

http://ftp-trace.ncbi.nlm.nih.gov/sra/ngs/1.3.0/ngs-sdk.1.3.0-linux.tar.gz

After extract and follow the instruction of this ngs-sdk.1.3.0-linux.tar.gz, I got this message :

~/RNAseq/tools/ngs-sdk.1.3.0-linux$ cd share
~/RNAseq/tools/ngs-sdk.1.3.0-linux/share$ make
make: uname: Command not found
make: true: Command not found
/home/atonidas/RNAseq/tools/ngs-sdk.1.3.0-linux/share/Makefile.config:53: recipe for target 'ncbi-headers' failed
make: *** [ncbi-headers] Error 127

Did I make something wrong? please advice, thank you so much

[GenoMax]

Are you doing this in MingW? If so use real linux since you installed it.

[atonidas]

Are you doing this in MingW? If so use real linux since you installed it.

nope, I did not do that in MinW, I did that in terminal of Linux.

[GenoMax]

Then why are common unix commands like "uname" not found?

Can you look in /bin to see if the uname and true commands are there? Also make sure /bin is in your $PATH.

[atonidas]

Then why are common unix commands like "uname" not found?

Can you look in /bin to see if the uname and true commands are there? Also make sure /bin is in your $PATH.

I set /home/atonidas/bin as my $PATH and I did installed all of my tools in there but there is no uname and true commands in that folder.

I have just installed ubuntu for 2 days and this is the first time of my life using this OS so that I really have no idea why common unix commands like "uname" are not there.

[GenoMax]

I am referring to /bin (which is the system bin not the one in your home directory). Can you check that directory?

[atonidas]

I just checked the computer/bin directory, and there are uname and true command in here. it's here.

[GenoMax]

So is that /bin directory in your $PATH. It normally should be (unless you changed the $PATH drastically). Put that directly back in there, if it is not present.

 export PATH=$PATH:\bin

[atonidas]

So is that /bin directory in your $PATH. It normally should be (unless you changed the $PATH drastically). Put that directly back in there, if it is not present.

 export PATH=$PATH:\bin

I am following your advice and I put everything back in there. Then I start compiling the "ngs-sdk.1.3.0-linux" again following the instruction and I got this message :

atonidas@atonidas:~/tool/ngs-sdk.1.3.0-linux/share$ make
c++   -g -o AlignSliceTest AlignSliceTest.cpp -L/usr/local/ngs/ngs-sdk/lib64/ -L/usr/local/ngs/ngs-sdk/lib64 -lncbi-ngs-c++ -lngs-c++ -lngs-bam-c++ -lncbi-ngs-c++ -lncbi-vdb-static -lngs-adapt-c++ -lpthread -ldl -lm 
AlignSliceTest.cpp:28:31: fatal error: ngs-bam/ngs-bam.hpp: No such file or directory
compilation terminated.
Makefile:84: recipe for target 'AlignSliceTest' failed
make: *** [AlignSliceTest] Error 1

I already add library directory to my LD_LIBRARY_PATH as instructed, but I still got the same message. I am not sure what happen

[GenoMax]

Perhaps you have a corrupted/incomplete download of the software. Can you re-download and try again?