Build Error on Docker Machine about bystro HOT 9 CLOSED

Where are you installing from? Try cd'ing into the bystro dir. Note install/install-go-packages.sh isn't found. This is clearly present in the cloned dir: https://github.com/akotlar/bystro/tree/b10/install

from bystro.

I am indeed in the bystro directory while building:

Step 11/13 : RUN . install/install-go-packages.sh
 ---> Running in 7700bf77c2b1
: not found install/install-go-packages.sh:
-e

Installing go packages (bystro-vcf, stats, snp)

: not found install/install-go-packages.sh:
: not found install/install-go-packages.sh:
: not found install/install-go-packages.sh:
Made /root/go path
: not found install/install-go-packages.sh:
: not found install/install-go-packages.sh:
: not found: install/install-go-packages.sh:
: not found: install/install-go-packages.sh:
: not found: install/install-go-packages.sh:
: not found: install/install-go-packages.sh:
: not found: install/install-go-packages.sh:
: not found: install/install-go-packages.sh:
The command '/bin/sh -c . install/install-go-packages.sh' returned a non-zero code: 127

mikof@DESKTOP-T2JVT0S MINGW64 ~/Documents/WINGO/docker/bystro (b10)
$ pwd
/c/Users/mikof/Documents/WINGO/docker/bystro

from bystro.

You did say that. Ok. I don't understand why Go wouldn't exist; it should be installed before than install-go-packages.sh RUN command: https://github.com/akotlar/bystro/blob/b10/Dockerfile#L13 . Something slightly weird is happening

from bystro.

Just an update: install/install-go-packages.sh as well as install/install-lmdb-linux.sh, which also had 'not-found' errors, are indeed in place at runtime.

Step 9/15 : RUN ls install/
 ---> Running in 0f0ad051b009
export-bystro-libs.sh
export-go-path-linux.sh
install-apt-deps.sh
install-go-linux.sh
install-go-mac.sh
install-go-packages.sh
install-liftover-linux.sh
install-lmdb-linux.sh
install-mac-deps.sh
install-perl-libs.sh
install-perlbrew-linux.sh
install-rpm-deps.sh
update-packages.sh

Additionally, go IS installed at runtime

Step 12/15 : RUN go version
 ---> Running in b8b9d08ef9c3
go version go1.11 linux/amd64

from bystro.

Solved: Running on windows, the DOS carriage returns get messed up on the two shell scripts. They should be converted to Unix before building. Following commands should do it:

awk '{ sub("\r$", ""); print }' install/install-lmdb-linux.sh > install/install-lmdb-linux.sh, awk '{ sub("\r$", ""); print }' install/install-go-packages.sh > install/install-go-packages.sh

from bystro.

Awesome work!

from bystro.

Oh wait...wtf. Why are \r present at all?

from bystro.

I think git auto-converts line endings either on clone or on checkout. Either that or you opened the files and re-saved.

Could you propose, PR an update to documentation to make sure LF line endings are preserved on clone?

Some proposals: https://help.github.com/en/articles/dealing-with-line-endings

Lets close this issue when that is done :)

from bystro.

PR sent: #57

Tested on local machine: all files that need to be LF now stay that way after clone.

from bystro.