installation error about speedseq HOT 6 OPEN

It looks like the submodules weren't cloned in. Did you clone it with "--recursive"?

git clone --recursive https://github.com/hall-lab/speedseq.git
cd speedseq
make

from speedseq.

Hello Colby,
I got similar error as follows,
cd src/parallel; ./configure --prefix=/data/software/speedseq-master
/bin/sh: ./configure: No such file or directory
make[1]: *** [parallel] Error 127
make[1]: Leaving directory `/data/software/speedseq-master'
make: *** [all] Error 2
I checked the src/parallel path, and it's empty. I tried to download the parallel code from “https://github.com/hall-lab/speedseq/tree/master/src”, but the file virtually do not exist. I wonder if the parallel file was broken or didn't upload successfully.

Looking forward to your reply. Thanks a lot.

from speedseq.

Is this after cloning with "--recursive"?

git clone --recursive https://github.com/hall-lab/speedseq.git
cd speedseq
make

from speedseq.

I tried to use this command, but it always stucked and only 26% can be downloaded, so I went to the web ( “https://github.com/hall-lab/speedseq/tree/master/src” ) and download it manually, somehow, the source code of parallel ( speedseq/src/parallel ) seems to be missing. Could you please check this file or if you have another way or URL to download.

[wenty-qq@node15 speedseq]$ git clone --recursive https://github.com/hall-lab/speedseq.git
Initialized empty Git repository in /public/analysis/wenty-qq/speedseq/speedseq/.git/
remote: Counting objects: 2652, done.
Receiving objects: 26% (705/2652), 1.31 MiB 5 KiB/s

many thanks

from speedseq.

I cannot replicate your issue with cloning the repo. I just ran git clone --recursive https://github.com/hall-lab/speedseq.git on my computer and it was successful.

By design, Github does not include submodules (like parallel) in the release directory. So you cannot download the full package from the releases page.

However, for your convenience I've temporary uploaded the entire SpeedSeq v0.1.2 package as a tarball.

from speedseq.

It works. Thank you so so much!

from speedseq.