Closed tonyjie closed 11 months ago
I found the problem is actually due to those .og
file is symlink when I clone the project.
exine depth -a -r t.gfa
doesn't help. It leads to MemoryError: std::bad_alloc
error.
But I build the t.og
on my own using odgi build
. Now odgi-py is able to load the .og
file.
Then I update the key of stages.calyx.exec
to be the absolute path.
Now I am able to go to the new error:
(py39) ➜ ~/Other_Repos/pollen/test git:(main) exine depth -a -r k.og
⠋ calyx.run_futil
⠙ calyx.run_futil
⠹ calyx.run_futil
⠸ calyx.run_futil
⠼ interpreter.interpret
[fud] ERROR: `/home/jl4257/Other_Repos/calyx/target/debug/interp --raw -l /home/jl4257/Other_Repos/calyx --data /tmp/tmpfznhcvmq/data.json /tmp/tmp8nqn8xuq' failed:
=====STDERR=====
/bin/sh: 1: /home/jl4257/Other_Repos/calyx/target/debug/interp: not found
=====STDOUT=====
Seems like this is due to my Calyx installation:
stages.interpreter.exec:
✖ /home/jl4257/Other_Repos/calyx/target/debug/interp not installed.
Is there any step that I missed? I installed Calyx from source following this.
Thank you for checking us out, Jiajie! It's very helpful as we try to take flight.
Sorry about the incorrect tip re: using .gfa
files. I realized it would not work and then deleted my message; didn't realize you had already seen it 😅
I think you've diagnosed this issue as well as I could have, so now I'd like to wait for @susan-garry to chime in and give us a solution. This stuff is her domain!
Susan, I think this may be a little additional nudge re: getting rid of those symlinked .og files. Earlier we thought it was just a stylistic issue, but the issue that Jiajie ran into may be more compelling than just style?
Hi, @tonyjie! Can you try doing cargo build -p interp
in the Calyx directory?
Hi, @tonyjie! Can you try doing
cargo build -p interp
in the Calyx directory?
It seems to solve my issue! Now exine depth -a -r k.og
can work!
Reopening: we should do some tidying in our text, and possibly some reorganization of our symlinked .og files, before closing this issue. Thanks @tonyjie!
Perhaps this is the place where we want to mention the need to build the Calyx interpreter: https://github.com/cucapra/pollen/blob/35c690df973269e9524147c9fe5fe689d1081433/README.md?plain=1#L42
Hi, I'm trying to run some Pollen before our meeting. I basically followed the installation guide for Pollen, Calyx, ODGI, and got an error when generating a node accelerator here. I think the error is still something related to ODGI-python binding.
Do you have any idea on how to fix this?
Error message
My current environment
import odgi
is successfull after I followed the detailed installation here from bioconda.fud check
shows the following messages.stages.calyx.exec: ✔ ./target/debug/calyx installed. ./target/debug/calyx is a relative path and will not work from every directory.
stages.interpreter.exec: ✖ /home/jl4257/Other_Repos/calyx/target/debug/interp not installed.
stages.dahlia.exec: ✖ dahlia not installed.
stages.verilog.exec: ✖ verilator not installed.
stages.vcd.exec: ✖ vcdump not installed.
stages.jq.exec: ✖ jq not installed.
stages.synth-verilog.exec: ✖ vivado not installed.
stages.vivado-hls.exec: ✖ vivado_hls not installed.
stages.futil.exec: ✔ /home/jl4257/Other_Repos/calyx/target/debug/futil installed.
interpreter, dahlia, verilog, vcd, jq, synth-verilog, vivado-hls were not installed correctly. Configuration instructions: https://docs.calyxir.org/fud/#configuration