sam2tsv add in my path

Question

[harry]

please can anyone tell me how to add sam2tsv in my path. I try the following command: export PATH="$PATH:/home/aclab/apps/jvarkit/dist/sam2tsv.jar" I also try this:

sudo mv /path/to/sam2tsv.jar /usr/local/bin/
sudo ln -s /usr/local/bin/sam2tsv.jar /usr/local/bin/sam2tsv
sudo nano /usr/local/bin/sam2tsv
#!/bin/bash
java -jar /usr/local/bin/sam2tsv.jar "$@"
sudo chmod +x /usr/local/bin/sam2tsv
sam2tsv --help

But none of them help can please solve this issue. thanks in advance

[Pierre Lindenbaum]

Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

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Answer 1

[Pierre Lindenbaum]

1) This is a JAR file, not an executable. So the first solution is useless.

2) In the second solution the sudo chmod +x is useless. Just run this sudo chmod +x /usr/local/bin/sam2ts once for this bash script which should only be:

#!/bin/bash
java -jar /path/to/sam2tsv.jar $@

3) unless you're working with a very old version of jvarkit , there is no such "sam2tsv.jar". The command should be:

java -jar /path/to/jvarkit.jar sam2tsv ...
`

[harry]

Hi so I download the latest version of java and jvarkit. but still i don't know how to move sam2tsv in my path. So I have not every time written whole command like other tools. Thanks in advance for solving the issue.

[Pierre Lindenbaum]

again, you don't need that shell script 'sam2tsv'. just run java -jar /path/to/jvarkit.jar sam2tsv ...

[Pierre Lindenbaum]

and acknowledge all your previous questions above.