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Error with installation #113
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I was just about to post the same issue. I'm installing Vt first time (Ubuntu 20.04) because I need it to decompose vcf files as input for another software I'm trying. My error logs are the exact same when I try
My Make version:
I hope there's a way to solve this! Thanks in advance! |
Eva, You may try a workaround using Conda, that worked for me, i.e.
regards, |
I installed it using miniconda, and it works for now. I just guess I have to get to the folder where the vt executable is saved to run it and then add file paths and so on to the commands. It seems to work. Thank you so much!! |
same issue with installation in dockerfile. Miniconda can only be used if you are using a centos based container. I was running vt in alpine container, and with this, its totally unusable |
hey @atks ... I'm also seeing the same issue and can't use Conda ... there is no lib/utils.c file and thus the compilation fails ... any workaround please ? |
yep, same error too :) |
For those with this particular issue, you can clone the repo and then: I.e. you go back to the previous "working" release 0.577 and then it should compile. Still, this issue should be adressed with a proper fix. |
Going back to release 0.577 results in a different error for me: In file included from bgzf.c:39: |
I got past this error by manually pulling the libdeflate from git. But there is an issue with the hts_utils.cpp file hts_utils.cpp: In function 'void bam_get_base_and_qual_and_read_and_qual(bam1_t*, uint32_t, char&, char&, int32_t&, kstring_t*, kstring_t*)': A workaround this is to add header --> #include "assert.h" in the "hts_utils.cpp" file. now i am stuck here. ahmm.o: In function |
@clarek20: marchoeppner's suggestion should work. See if installing libz-dev (or the corresponding package for your OS) solves your issue. |
I got similar experiences with compiling vt after cloning it from github. Now, instead of compiling vt-master, |
Hi,
I have used your nice tool for a long time, downloading and installing within a Dockerfile. It has worked perfect for my purposes (multiallelic variant decomposition). However, I am now unable to compile with
make
for some reason, not really sure why it's now complaining:cd lib/libdeflate; make || exit 1;
make[1]: Entering directory '/data/sigven/software/vt/lib/libdeflate'
CC lib/deflate_decompress.o
make[1]: *** No rule to make target 'lib/utils.c', needed by 'lib/utils.o'. Stop.
make[1]: Leaving directory '/data/sigven/software/vt/lib/libdeflate'
make: *** [Makefile:151: lib/libdeflate/libdeflate.a] Error 1
Make version:
GNU Make 4.3
Any idea what's the problem?
thanks,
Sigve
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