mapostolides
commented
4 years ago Hi everyone,
I got STAR-SEQR version 0.6.7 running! I was able to extract the tool versions from the following docker container:
docker://eagenomics/starseqr:0.6.7
Not sure if all these tools are required, but I didn't want to touch it. I made a couple of changes to it when installing starseqr.py.
# This file may be used to create an environment using:
# $ conda create --name <env> --file <this file>
# platform: linux-64
_libgcc_mutex=0.1=conda_forge
_openmp_mutex=4.5=0_gnu
asn1crypto=0.22.0=py27_0
bcftools=1.9=h47928c2_2
biobambam=2.0.87=1
blas=1.0=mkl
boost=1.64.0=py27_4
boost-cpp=1.64.0=1
bzip2=1.0.8=h516909a_2
ca-certificates=2020.4.5.1=hecc5488_0
cffi=1.10.0=py27_0
conda=4.3.30=py27h6ae6dc7_0
conda-env=2.6.0=0
coverage=4.4.1=py27_0
cryptography=1.8.1=py27_0
curl=7.61.0=h93b3f91_2
cython=0.26=py27_0
decorator=4.1.2=py27_0
enum34=1.1.6=py27_0
gffread=0.9.9=1
htslib=1.9=hc238db4_4
icu=58.2=0
idna=2.6=py27_0
intervaltree=2.1.0=py27_0
intervaltree_bio=1.0.1=py_1
ipaddress=1.0.18=py27_0
jemalloc=4.5.0=0
krb5=1.14.6=0
libdeflate=1.0=h470a237_0
libffi=3.2.1=1
libgcc=5.2.0=0
libgcc-ng=9.2.0=h24d8f2e_2
libgomp=9.2.0=h24d8f2e_2
libpng=1.6.35=ha92aebf_2
libssh2=1.8.0=0
libstdcxx-ng=9.2.0=hdf63c60_2
libuuid=1.0.3=0
mkl=2017.0.3=0
mysql-connector-c=6.1.6=2
ncurses=6.1=hfc679d8_1
networkx=2.0=py27_1
nose=1.3.7=py27_1
numpy=1.13.1=py27_0
openssl=1.0.2u=h516909a_0
packaging=16.8=py27_0
pandas=0.20.3=py27_0
pip=9.0.1=py27_1
primer3-py=0.6.0=py27h516909a_0
pycosat=0.6.1=py27_1
pycparser=2.18=py27_0
pycrypto=2.6.1=py27_4
pyopenssl=17.0.0=py27_0
pyparsing=2.2.0=py27_0
pysam=0.15.1=py27h0380709_0
python=2.7.12=1
python-dateutil=2.6.1=py27_0
pytz=2017.2=py27_0
pyyaml=3.11=py27_4
readline=6.2=2
requests=2.14.2=py27_0
ruamel_yaml=0.11.14=py27_0
salmon=0.9.1=1
samtools=1.9=h8ee4bcc_1
setuptools=23.0.0=py27_0
six=1.10.0=py27_0
sortedcontainers=2.1.0=py_0
sqlite=3.13.0=0
star=2.5.4a=0
starseqr=0.6.7=py27h7eb728f_0
tbb=2019.0=h2d50403_0
tk=8.5.18=0
ucsc-gtftogenepred=366=h5eb252a_0
velvet=1.2.10=h470a237_2
wheel=0.29.0=py27_0
xz=5.2.4=h470a237_1
yaml=0.1.6=0
zlib=1.2.11=0
Hi, it seems that STAR-SEQR might no longer be useable with most recent versions of its dependencies. I have installed it via bioconda as per the following website, and keep running into roadblocks with deprecations and updated tools that have changed, and are no longer compatible with "starseqr.py" and its "starseqr_utils" library:
https://bioconda.github.io/recipes/starseqr/README.html
Is there anywhere that I can find a complete listing of all dependencies with exact tool versions for which STAR-SEQR has been tested and completely worked?
Thanks!