Comments (7)
Thank you! Going to see if I can replicate on my end!
from dragonflye.
Hi @valery-shap I'm going to go ahead and close this, please feel free to reopen if you think its needed!
from dragonflye.
Hi @valery-shap,
Can you post the contents of conda env export
while in your base environment? I'm also going to try and replicate locally on my end.
Cheers,
Robert
from dragonflye.
name: base
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=1_gnu
- arrow=0.17.0=py38h578d9bd_1
- attrs=20.3.0=pyhd3deb0d_0
- backports=1.0=py_2
- backports.functools_lru_cache=1.6.1=py_0
- binaryornot=0.4.4=py_1
- bzip2=1.0.8=h7f98852_4
- c-ares=1.18.1=h7f98852_0
- ca-certificates=2021.10.8=ha878542_0
- certifi=2021.10.8=py38h578d9bd_1
- cffi=1.14.0=py38he30daa8_1
- chardet=3.0.4=py38_1003
- click=7.1.2=pyh9f0ad1d_0
- colorama=0.4.4=pyh9f0ad1d_0
- commonmark=0.9.1=py_0
- conda=4.11.0=py38h578d9bd_0
- conda-package-handling=1.6.1=py38h7b6447c_0
- cookiecutter=1.7.2=pyh9f0ad1d_0
- coreutils=8.25=1
- cryptography=2.9.2=py38h1ba5d50_0
- curl=7.78.0=h1ccaba5_0
- expat=2.2.10=he6710b0_2
- future=0.18.2=py38h578d9bd_3
- git=2.23.0=pl526hacde149_0
- gitdb=4.0.5=pyhd8ed1ab_1
- gitpython=3.1.13=pyhd8ed1ab_0
- icu=68.2=h9c3ff4c_0
- idna=2.9=py_1
- importlib-metadata=3.4.0=py38h578d9bd_0
- importlib_metadata=3.4.0=hd8ed1ab_0
- jinja2=2.11.3=pyh44b312d_0
- jinja2-time=0.2.0=py_2
- jsonschema=3.2.0=py_2
- krb5=1.19.2=hac12032_0
- ld_impl_linux-64=2.33.1=h53a641e_7
- libarchive=3.5.2=hccf745f_1
- libcurl=7.78.0=h0b77cf5_0
- libedit=3.1.20210910=h7f8727e_0
- libev=4.33=h516909a_1
- libffi=3.3=he6710b0_1
- libgcc=7.2.0=h69d50b8_2
- libgcc-ng=11.2.0=h1d223b6_11
- libgomp=11.2.0=h1d223b6_11
- libiconv=1.16=h516909a_0
- libnghttp2=1.43.0=h812cca2_1
- libsolv=0.7.19=h780b84a_5
- libssh2=1.9.0=hab1572f_5
- libstdcxx-ng=11.2.0=he4da1e4_11
- libxml2=2.9.12=h72842e0_0
- lz4-c=1.9.3=h9c3ff4c_1
- lzo=2.10=h516909a_1000
- mamba=0.15.3=py38h2aa5da1_0
- markupsafe=1.1.1=py38h8df0ef7_2
- ncurses=6.3=h7f8727e_2
- nextflow=20.10.0=hecda079_0
- nf-core=1.12.1=pyh3252c3a_0
- openjdk=10.0.2=h14c3975_1015
- openssl=1.1.1l=h7f98852_0
- pcre=8.44=he1b5a44_0
- perl=5.32.0=h36c2ea0_0
- pip=20.0.2=py38_3
- poyo=0.5.0=py_0
- prompt-toolkit=3.0.16=pyha770c72_0
- prompt_toolkit=3.0.16=hd8ed1ab_0
- pycosat=0.6.3=py38h7b6447c_1
- pycparser=2.20=py_0
- pygments=2.8.0=pyhd8ed1ab_0
- pyopenssl=19.1.0=py38_0
- pyrsistent=0.17.3=py38h25fe258_1
- pysocks=1.7.1=py38_0
- python=3.8.3=hcff3b4d_0
- python-dateutil=2.8.1=py_0
- python-slugify=4.0.1=pyh9f0ad1d_0
- python_abi=3.8=1_cp38
- pyyaml=5.1.2=py38h516909a_0
- questionary=1.9.0=pyhd8ed1ab_0
- readline=8.0=h7b6447c_0
- reproc=14.2.3=h7f98852_0
- reproc-cpp=14.2.3=h9c3ff4c_0
- requests=2.23.0=py38_0
- requests-cache=0.5.0=py_0
- rich=9.11.1=py38h578d9bd_0
- ruamel_yaml=0.15.87=py38h7b6447c_0
- setuptools=46.4.0=py38_0
- six=1.14.0=py38_0
- smmap=3.0.5=pyh44b312d_0
- sqlite=3.31.1=h62c20be_1
- tabulate=0.8.9=pyhd8ed1ab_0
- text-unidecode=1.3=py_0
- tk=8.6.8=hbc83047_0
- tqdm=4.46.0=py_0
- typing_extensions=3.7.4.3=py_0
- unidecode=1.2.0=pyhd8ed1ab_0
- urllib3=1.25.8=py38_0
- wcwidth=0.2.5=pyh9f0ad1d_2
- wheel=0.34.2=py38_0
- whichcraft=0.6.1=py_0
- xz=5.2.5=h7b6447c_0
- yaml=0.1.7=had09818_2
- zipp=3.4.0=py_0
- zlib=1.2.11=h7b6447c_3
- zstd=1.5.0=ha95c52a_0
prefix: /home/vshapovalova/miniconda3
from dragonflye.
Good news! I was able to replicate (also apologies on the delay getting to this). I gave up after ~10 minutes of solving
conda install -c conda-forge -c bioconda dragonflye
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
I retried with Mamba,
mamba install -c conda-forge -c bioconda dragonflye
And ran into this issue:
Pinned packages:
- python 3.9.*
Encountered problems while solving:
- package dragonflye-1.0.6-hdfd78af_0 requires medaka >=1.4.4, but none of the providers can be installed
I'm going to review the dependencies. Looks like the issue is one updated to require >3.9.*
, while medaka requires <3.9
.
Will update sooner this time!
from dragonflye.
Interesting development, I'm unable to install dragonflye using Mamba v0.15.3, but can do so with Mamba v0.24.0
conda install -c conda-forge -c bioconda 'mamba>=0.24.0'
mamba create -n test-dragonflye -c conda-forge -c bioconda dragonflye
__ __ __ __
/ \ / \ / \ / \
/ \/ \/ \/ \
███████████████/ /██/ /██/ /██/ /████████████████████████
/ / \ / \ / \ / \ \____
/ / \_/ \_/ \_/ \ o \__,
/ _/ \_____/ `
|/
███╗ ███╗ █████╗ ███╗ ███╗██████╗ █████╗
████╗ ████║██╔══██╗████╗ ████║██╔══██╗██╔══██╗
██╔████╔██║███████║██╔████╔██║██████╔╝███████║
██║╚██╔╝██║██╔══██║██║╚██╔╝██║██╔══██╗██╔══██║
██║ ╚═╝ ██║██║ ██║██║ ╚═╝ ██║██████╔╝██║ ██║
╚═╝ ╚═╝╚═╝ ╚═╝╚═╝ ╚═╝╚═════╝ ╚═╝ ╚═╝
mamba (0.24.0) supported by @QuantStack
GitHub: https://github.com/mamba-org/mamba
Twitter: https://twitter.com/QuantStack
█████████████████████████████████████████████████████████████
Looking for: ['dragonflye']
bioconda/noarch 3.7MB @ 3.0MB/s 1.3s
pkgs/main/linux-64 4.8MB @ 3.5MB/s 1.5s
pkgs/r/noarch No change
pkgs/main/noarch No change
pkgs/r/linux-64 No change
bioconda/linux-64 4.3MB @ 1.9MB/s 2.3s
conda-forge/noarch 9.3MB @ 3.1MB/s 3.1s
conda-forge/linux-64 25.4MB @ 3.2MB/s 8.3s
Transaction
Prefix: /home/robert_petit/miniconda3/envs/test-dragonflye
Updating specs:
- dragonflye
... TRUNCATED ...
Summary:
Install: 205 packages
Total download: 1GB
──────────────────────────────────────────────────────────────────────────────────────────────────────
Confirm changes: [Y/n]
from dragonflye.
Thank you for reply! I have mamba (0.15.3) and I was able to install bactopia using it. (conda didn't work for it too)
It is not about the topic this issue, but I noticed that dragonflye threw away small plasmids like ColRNA(less than 10kb) more often than Unicycler pipeline with long reads only. I will check during what step it happens, so maybe this difference is only because of different performance of flye or miniasm assemblers. And sometimes Unicycler is not able to assemble the whole chromosome unlike Flye. If it is so, the ideal receipt of using dragonflye tool could be to have 3 different assemblies with flye, miniasm and raven. And choose the better one.
Best regards,
Valery
from dragonflye.
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