Install STAR-Fusion inside Conda (Snakemake) fails

Question

[Nathalie]

Hi everyone,

I'm trying to install STAR-Fusion inside a Conda image (Snakemake) to run it inside a pipeline. However, I get some troubles when I try to compile it inside my Conda image :

(snakemake) NJEANRAY@OCS-NJE:~/Gene_Fusion/STAR-Fusion$ make
cd plugins && make
make[1] : on entre dans le répertoire « /home/ldap/NJEANRAY/Gene_Fusion/STAR-Fusion/plugins »
tar xvf Set-IntervalTree-0.01.tar.gz && \
       cd Set-IntervalTree-0.01 && \
       perl Makefile.PL && \
       make && \
       mv lib/Set ../../PerlLib/ && \
       mv blib/arch/auto ../../PerlLib && \
       mv blib/lib/auto/Set/IntervalTree/autosplit.ix ../../PerlLib/auto/Set/IntervalTree/.
Set-IntervalTree-0.01/
Set-IntervalTree-0.01/src/
Set-IntervalTree-0.01/src/Makefile
Set-IntervalTree-0.01/src/interval_tree.h
Set-IntervalTree-0.01/src/test_main.cc
Set-IntervalTree-0.01/lib/
Set-IntervalTree-0.01/lib/Set/
Set-IntervalTree-0.01/lib/Set/IntervalTree.pm
Set-IntervalTree-0.01/Changes
Set-IntervalTree-0.01/MANIFEST
Set-IntervalTree-0.01/t/
Set-IntervalTree-0.01/t/Set-IntervalTree.t
Set-IntervalTree-0.01/typemap
Set-IntervalTree-0.01/perlobject.map
Set-IntervalTree-0.01/IntervalTree.xs
Set-IntervalTree-0.01/Makefile.PL
Set-IntervalTree-0.01/README
Set-IntervalTree-0.01/META.yml
Generating a Unix-style Makefile
Writing Makefile for Set::IntervalTree
Writing MYMETA.yml and MYMETA.json
make[2] : on entre dans le répertoire « /home/ldap/NJEANRAY/Gene_Fusion/STAR-Fusion/plugins/Set-IntervalTree-0.01 »
Skip blib/lib/Set/IntervalTree.pm (unchanged)
Running Mkbootstrap for IntervalTree ()
chmod 644 "IntervalTree.bs"
"/home/ldap/NJEANRAY/anaconda3/envs/snakemake/bin/perl" -MExtUtils::Command::MM -e 'cp_nonempty' -- IntervalTree.bs blib/arch/auto/Set/IntervalTree/IntervalTree.bs 644
g++ -c  -Isrc -D_REENTRANT -D_GNU_SOURCE -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/ldap/NJEANRAY/anaconda3/envs/snakemake/include -fdebug-prefix-map=/home/conda/feedstock_root/build_artifacts/perl_1622804860086/work=/usr/local/src/conda/perl-5.32.1 -fdebug-prefix-map=/home/ldap/NJEANRAY/anaconda3/envs/snakemake=/usr/local/src/conda-prefix -D_REENTRANT -D_GNU_SOURCE -fwrapv -fno-strict-aliasing -pipe -fstack-protector-strong -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -D_FORTIFY_SOURCE=2 -D_LARGEFILE_SOURCE -D_FILE_OFFSET_BITS=64 -g -O0   -DVERSION=\"0.01\" -DXS_VERSION=\"0.01\" -fPIC --sysroot=/bin/..//x86_64-conda-linux-gnu/sysroot "-I/home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/5.32/core_perl/CORE"  -Isrc IntervalTree.c
In file included from IntervalTree.xs:6:
/home/ldap/NJEANRAY/anaconda3/envs/snakemake/lib/perl5/5.32/core_perl/CORE/perl.h:822:10: fatal **error: sys/types.h: Aucun fichier ou dossier de ce type
  822 | #include <sys/types.h>
      |          ^~~~~~~~~~~~~**
compilation terminated.
make[2]: *** [Makefile:341 : IntervalTree.o] Erreur 1
make[2] : on quitte le répertoire « /home/ldap/NJEANRAY/Gene_Fusion/STAR-Fusion/plugins/Set-IntervalTree-0.01 »
make[1]: *** [Makefile:3 : all] Erreur 2
make[1] : on quitte le répertoire « /home/ldap/NJEANRAY/Gene_Fusion/STAR-Fusion/plugins »
make: *** [Makefile:3 : all] Erreur 2

Indeed, I've installed sucessfully all the Perl libraries mentioned in the STAR-Fusion website.

Here is my settings :

• Ubuntu 20.04.2 LTS
• Conda : 4.10.1
• STAR : 2.7.9a
• STAR-Fusion : 1.10.0
• g++ : 9.3.0

Could you please advice ?

Thanks a lot !

Best regards, Nathalie

[ATpoint]

What is a conda "image"? There are container images, but conda environments. Do you mean Singularity image? If you are using conda anyway, why do you compile it rather than just using conda itself?

https://anaconda.org/bioconda/star-fusion