Hi,
So I am trying to use SequenceTubeMap (a vgteam software) and I am trying to download its dependencies. However, I am struggling to clone VG. I get so many errors and dependencies getting failed. So let's start:
Using git: For git there are two commands that I have tried:
1. git clone --recursive https://github.com/vgteam/vg.git
2. git clone https://github.com/vgteam/vg.git
- The first one has the following error:
I tried to find elfutils to download it manually but I cannot find it.Cloning into '/home/userpc414/Documents/programs/vg/deps/elfutils'... fatal: unable to connect to sourceware.org: sourceware.org[0: 8.43.85.97]: errno=Connection timed out sourceware.org[1: 2620:52:3:1:0:246e:9693:128c]: errno=Network is unreachable fatal: clone of 'git://sourceware.org/git/elfutils.git' into submodule path '/home/userpc414/Documents/programs/vg/deps/elfutils' failed Failed to clone 'deps/elfutils' a second time, aborting For the second one, I get this error:
make: No rule to make target 'lib/libsdsl.a', needed by 'obj/aligner.o'. Stop.then I checked the dependencies of vg and I saw some dependencies were missing and I wanted to download them one by one, but then I had cmake errors in some of the downloads putting me into a loop of debugging. Something like a problem within a problem within a problem.
Example:cmake -H. -Bbuild && cmake --build build -- -j4 CMake Error at /usr/share/cmake-3.22/Modules/ExternalProject.cmake:2882 (message): No download info given for 'handlegraph' and its source directory:this was an error created by a xg dependency that was missing
Using tarfiles: Here I downloaded the latest release of vg --> vg-v1.57.0.tar.gz this one was the most promising but I get the following error:
htscodecs/htscodecs/htscodecs.c: In function ‘htscodecs_version’:
htscodecs/htscodecs/htscodecs.c:43:12: error: ‘HTSCODECS_VERSION_TEXT’ undeclared (first use in this function); did you mean ‘HTSCODECS_VERSION’?
43 | return HTSCODECS_VERSION_TEXT;
| ^~~~~~~~~~~~~~~~~~~~~~
| HTSCODECS_VERSION
htscodecs/htscodecs/htscodecs.c:43:12: note: each undeclared identifier is reported only once for each function it appears in
htscodecs/htscodecs/htscodecs.c:44:1: warning: control reaches end of non-void function [-Wreturn-type]
44 | }
| ^
make[1]: *** [Makefile:160: htscodecs/htscodecs/htscodecs.o] Error 1
make[1]: Leaving directory '/home/userpc414/Documents/programs/vg-v1.40.0/deps/htslib'
make: *** [Makefile:567: lib/libhts.a] Error 2
The only way that I managed to download vg is using conda, however since my primary goal is to download SequenceTube and vg is on the dependencies, I couldn't proceed. I would appreciate any help on this.
Solution that I used: run SequenceTube thorugh the conda environment were the vg has been downloaded.
1 answer
Hey everyone,
I wanted to thank you all for your immediate responses and insights. You're absolutely right about the misleading title, and I should have focused on highlighting the SequenceTubeMap install issue from the start. I apologize for any confusion caused by that. Admittedly, I might have been a bit dramatic in my frustration, so I appreciate your patience.
As an update, I was able to download the binaries, but unfortunately, SequenceTubeMap still didn't cooperate (error vg chunk and vg view failed--check thread). However, following your suggestion to use conda, everything worked flawlessly. The git clone --recursive https://github.com/vgteam/vg.git unfortunately crashes in the elfutils step. I found this thread on Github with a similar problem that suggests manually cloning the elfutils. However, thank you for your time and also for pointing me in the right direction! Also sorry once more for the misleading message.
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Why are you not downloading the
vgbinaries provided here: https://github.com/vgteam/vg/releases/tag/v1.57.0 Use theClick here to Downloadbutton.I just downloaded and verified that binary works on RHEL.
Also, OP buries the lede and uses a misleading title. They are able to install vg using conda, but that is secondary to them using a different tool, which should be the one mentioned in the title, not vg.
I read that to mean that the only way they were able to download
vgwas by usingconda. SinceSequenceTube(whatever that is) requiresvgto be there that may be in convenient since they will need to have the conda env active.SequenceTubeis likely not available viacondaotherwise it would have taken care of gettingvgautomatically.In that case, OP should have said "Cannot install SequenceTube", since that is the problem, not vg.
Maybe this is the SequenceTube that OP is referring to? https://github.com/vgteam/sequenceTubeMap. In any case, like you say, having the conda env active should solve their problem.
You're mentioning this as a footnote when it should be the headline. Your post title says "I cannot download VG in any way" which you yourself demonstrate to be false in multiple ways in your post. Please be accurate, not dramatic.
Downloading the binary as GenoMax (and the vgteam) suggests is most likely the best option. For the record,
git clone --recursive https://github.com/vgteam/vg.gitworks for me but it did sit a minute or so atCloning into '/home/userpc414/Documents/programs/vg/deps/elfutils'...so maybe the errorerrno=Connection timed outis only a sporadic failure. But again, I would leave compiling from source as a last resort.