VG view and VG chunk failed when using SequenceTubeMap

Question

[gforg34]

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

1. The first one has the following error:

    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
   

   I tried to find elfutils to download it manually but I cannot find it.

2. 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.

[GenoMax]

Why are you not downloading the vg binaries provided here: https://github.com/vgteam/vg/releases/tag/v1.57.0 Use the Click here to Download button.

I just downloaded and verified that binary works on RHEL.

[Ram]

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.

[GenoMax]

I read that to mean that the only way they were able to download vg was by using conda. Since SequenceTube (whatever that is) requires vg to be there that may be in convenient since they will need to have the conda env active. SequenceTube is likely not available via conda otherwise it would have taken care of getting vg automatically.

[Ram]

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.

[Ram]

The only way that I managed to download vg is using conda, however since my primary goal is to download SequenceTube

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.

[dariober]

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.git works for me but it did sit a minute or so at Cloning into '/home/userpc414/Documents/programs/vg/deps/elfutils'... so maybe the error errno=Connection timed out is only a sporadic failure. But again, I would leave compiling from source as a last resort.

Answer 1

[gforg34]

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.

[GenoMax]

VG view and VG chunk failed when using SequenceTubeMap

You changed the title to the latest problem you are encountering, which does not match the content of your original post. So for a future visitor this thread is now confusing.

[gforg34]

Yes I did changed it to the actual problem, because I agreed that the problem did not align with the title as you also mentioned. If you have any suggestions for the title please let me know.