Kiliankleemann commented 8 months ago

Would love to try your tool! Got this error for installation:

UnsatisfiableError: The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.35=0
  - python=3.10 -> libgcc-ng[version='>=10.3.0'] -> __glibc[version='>=2.17']

Your installed version is: 2.35

Note that strict channel priority may have removed packages required for satisfiability.

shunhuahan commented 8 months ago

Hi @Kiliankleemann,

Thanks for your report! Could I ask what are the command lines you used for installing TELR?

I just tried installing TELR under a new environment using mamba, the installation worked successfully. Here is the command line I used. Could you try this and let me know if this works for you?

mamba create -n TELR --channel bioconda telr

Kiliankleemann commented 8 months ago

Is it a must to install with mamba? I have trouble setting up mamba.

Kiliankleemann commented 8 months ago

I installed mamba now in a new environment which I set up with CONDASUBDIR=linux-64. Then I ran

mamba install telr


The following package could not be installed
└─ telr is installable and it requires
   └─ rmblast 2.6.0.* , which requires
      └─ boost >=1.67.0,<1.67.1.0a0  with the potential options
         ├─ boost 1.67.0 would require
         │  └─ python [2.7* |>=2.7,<2.8.0a0 ], which can be installed;
         ├─ boost 1.67.0 would require
         │  └─ python [3.5* |>=3.5,<3.6.0a0 ], which can be installed;
         ├─ boost 1.67.0 would require
         │  └─ python 3.6* , which can be installed;
         ├─ boost 1.67.0 would require
         │  └─ python >=3.6,<3.7.0a0 , which can be installed;
         └─ boost 1.67.0 conflicts with any installable versions previously reported.

shunhuahan commented 8 months ago

@Kiliankleemann It seems that I can not reproduce this error by following the same steps that you used for installation, but there are two things I want to check with you to help resolve the issue.

Have you added the proper channels to your conda before the installation?

conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge

You might have an older cache of packages from mamba that might be causing the problem. Could you try running mamba clean --all to clean up any old packages and caches and then try again?
If none of them works, could you send me an email (hanshunhua0829@gmail.com) and I can figure out a better way for you to get access to TELR, potentially by sharing a docker container with the latest version of TELR and all dependencies included.

Thanks, Shunhua

shunhuahan commented 8 months ago

@Kiliankleemann and to this question "Is it a must to install with mamba? I have trouble setting up mamba."

No, mamba is just an alternative to conda that allows faster installation. If there are mamba setup issues in your environment, I would also suggest trying conda create -n TELR --channel bioconda telr and see if it works for you. Thanks!

Kiliankleemann commented 8 months ago

Thank you for the responses! I also tried conda create -n TELR --channel bioconda telr but my conda just keeps searching and not downloading. I installed mamba now and it works.

Kiliankleemann commented 8 months ago

I seemed to have installed telr but still get errors.

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bcftools                  1.18                 h8b25389_0    bioconda
bedtools                  2.31.0               hf5e1c6e_3    bioconda
biopython                 1.81            py310h1fa729e_0    conda-forge
boltons                   23.0.0             pyhd8ed1ab_0    conda-forge
brotli                    1.1.0                hd590300_1    conda-forge
brotli-bin                1.1.0                hd590300_1    conda-forge
brotli-python             1.1.0           py310hc6cd4ac_1    conda-forge
bzip2                     1.0.8                h7f98852_4    conda-forge
c-ares                    1.20.1               hd590300_0    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
certifi                   2023.7.22          pyhd8ed1ab_0    conda-forge
cffi                      1.16.0          py310h2fee648_0    conda-forge
charset-normalizer        3.3.0              pyhd8ed1ab_0    conda-forge
colorama                  0.4.6              pyhd8ed1ab_0    conda-forge
conda                     23.9.0          py310hff52083_0    conda-forge
conda-package-handling    2.2.0              pyh38be061_0    conda-forge
conda-package-streaming   0.9.0              pyhd8ed1ab_0    conda-forge
contourpy                 1.1.1           py310hd41b1e2_1    conda-forge
cryptography              41.0.4          py310h75e40e8_0    conda-forge
cycler                    0.12.1             pyhd8ed1ab_0    conda-forge
cython                    3.0.3                    pypi_0    pypi
fmt                       10.1.1               h00ab1b0_0    conda-forge
fonttools                 4.43.1          py310h2372a71_0    conda-forge
freetype                  2.12.1               h267a509_2    conda-forge
gffcompare                0.12.6               h4ac6f70_2    bioconda
gsl                       2.7                  he838d99_0    conda-forge
htslib                    1.18                 h81da01d_0    bioconda
icu                       73.2                 h59595ed_0    conda-forge
idna                      3.4                pyhd8ed1ab_0    conda-forge
intervaltree              3.1.0              pyhd8ed1ab_1    conda-forge
jsonpatch                 1.33               pyhd8ed1ab_0    conda-forge
jsonpointer               2.4             py310hff52083_3    conda-forge
k8                        0.2.5                hdcf5f25_4    bioconda
keyutils                  1.6.1                h166bdaf_0    conda-forge
kiwisolver                1.4.5           py310hd41b1e2_1    conda-forge
krb5                      1.21.2               h659d440_0    conda-forge
lcms2                     2.15                 h7f713cb_2    conda-forge
ld_impl_linux-64          2.40                 h41732ed_0    conda-forge
lerc                      4.0.0                h27087fc_0    conda-forge
libarchive                3.7.2                h039dbb9_0    conda-forge
libblas                   3.9.0           18_linux64_openblas    conda-forge
libbrotlicommon           1.1.0                hd590300_1    conda-forge
libbrotlidec              1.1.0                hd590300_1    conda-forge
libbrotlienc              1.1.0                hd590300_1    conda-forge
libcblas                  3.9.0           18_linux64_openblas    conda-forge
libcurl                   8.4.0                hca28451_0    conda-forge
libdeflate                1.18                 h0b41bf4_0    conda-forge
libedit                   3.1.20191231         he28a2e2_2    conda-forge
libev                     4.33                 h516909a_1    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc-ng                 13.2.0               h807b86a_2    conda-forge
libgfortran-ng            13.2.0               h69a702a_2    conda-forge
libgfortran5              13.2.0               ha4646dd_2    conda-forge
libgomp                   13.2.0               h807b86a_2    conda-forge
libiconv                  1.17                 h166bdaf_0    conda-forge
libjpeg-turbo             2.1.5.1              hd590300_1    conda-forge
liblapack                 3.9.0           18_linux64_openblas    conda-forge
libmamba                  1.5.2                had39da4_0    conda-forge
libmambapy                1.5.2           py310h39ff949_0    conda-forge
libnghttp2                1.52.0               h61bc06f_0    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libopenblas               0.3.24          pthreads_h413a1c8_0    conda-forge
libpng                    1.6.39               h753d276_0    conda-forge
libsolv                   0.7.25               hfc55251_0    conda-forge
libsqlite                 3.43.2               h2797004_0    conda-forge
libssh2                   1.11.0               h0841786_0    conda-forge
libstdcxx-ng              13.2.0               h7e041cc_2    conda-forge
libtiff                   4.6.0                h8b53f26_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libwebp-base              1.3.2                hd590300_0    conda-forge
libxcb                    1.15                 h0b41bf4_0    conda-forge
libxml2                   2.11.5               h232c23b_1    conda-forge
libzlib                   1.2.13               hd590300_5    conda-forge
lz4-c                     1.9.4                hcb278e6_0    conda-forge
lzo                       2.10              h516909a_1000    conda-forge
mamba                     1.5.2           py310h51d5547_0    conda-forge
matplotlib-base           3.8.0           py310h62c0568_2    conda-forge
miniasm                   0.3                  he4a0461_2    bioconda
minimap2                  2.26                 he4a0461_2    bioconda
munkres                   1.1.4              pyh9f0ad1d_0    conda-forge
ncls                      0.0.68          py310h4b81fae_1    bioconda
ncurses                   6.4                  hcb278e6_0    conda-forge
numpy                     1.26.0          py310hb13e2d6_0    conda-forge
openjpeg                  2.5.0                h488ebb8_3    conda-forge
openssl                   3.1.3                hd590300_0    conda-forge
packaging                 23.2               pyhd8ed1ab_0    conda-forge
pandas                    2.1.1           py310hcc13569_1    conda-forge
perl                      5.32.1          4_hd590300_perl5    conda-forge
pillow                    10.0.1          py310h29da1c1_1    conda-forge
pip                       23.3               pyhd8ed1ab_0    conda-forge
pluggy                    1.3.0              pyhd8ed1ab_0    conda-forge
pomoxis                   0.3.13             pyhdfd78af_0    bioconda
porechop                  0.2.4           py310h0dbaff4_6    bioconda
pthread-stubs             0.4               h36c2ea0_1001    conda-forge
pybind11-abi              4                    hd8ed1ab_3    conda-forge
pycosat                   0.6.6           py310h2372a71_0    conda-forge
pycparser                 2.21               pyhd8ed1ab_0    conda-forge
pyopenssl                 23.2.0             pyhd8ed1ab_1    conda-forge
pyparsing                 3.1.1              pyhd8ed1ab_0    conda-forge
pysam                     0.21.0          py310h41dec4a_1    bioconda
pysocks                   1.7.1              pyha2e5f31_6    conda-forge
python                    3.10.12         hd12c33a_0_cpython    conda-forge
python-dateutil           2.8.2              pyhd8ed1ab_0    conda-forge
python-tzdata             2023.3             pyhd8ed1ab_0    conda-forge
python_abi                3.10                    4_cp310    conda-forge
pytz                      2023.3.post1       pyhd8ed1ab_0    conda-forge
racon                     1.5.0                h21ec9f0_2    bioconda
readline                  8.2                  h8228510_1    conda-forge
reproc                    14.2.4.post0         hd590300_0    conda-forge
reproc-cpp                14.2.4.post0         h59595ed_0    conda-forge
requests                  2.31.0             pyhd8ed1ab_0    conda-forge
ruamel.yaml               0.17.35         py310h2372a71_0    conda-forge
ruamel.yaml.clib          0.2.7           py310h2372a71_2    conda-forge
samtools                  1.18                 h50ea8bc_1    bioconda
seqkit                    2.5.1                h9ee0642_0    bioconda
setuptools                68.2.2             pyhd8ed1ab_0    conda-forge
six                       1.16.0             pyh6c4a22f_0    conda-forge
sortedcontainers          2.4.0              pyhd8ed1ab_0    conda-forge
stringtie                 2.2.1                h6b7c446_4    bioconda
telr                      1.0                      pypi_0    pypi
tk                        8.6.13               h2797004_0    conda-forge
tqdm                      4.66.1             pyhd8ed1ab_0    conda-forge
truststore                0.8.0              pyhd8ed1ab_0    conda-forge
tzdata                    2023c                h71feb2d_0    conda-forge
unicodedata2              15.1.0          py310h2372a71_0    conda-forge
urllib3                   2.0.6              pyhd8ed1ab_0    conda-forge
wheel                     0.41.2             pyhd8ed1ab_0    conda-forge
xorg-libxau               1.0.11               hd590300_0    conda-forge
xorg-libxdmcp             1.1.3                h7f98852_0    conda-forge
xz                        5.2.6                h166bdaf_0    conda-forge
yaml-cpp                  0.8.0                h59595ed_0    conda-forge
zlib                      1.2.13               hd590300_5    conda-forge
zstandard                 0.21.0          py310h1275a96_1    conda-forge
zstd                      1.5.5                hfc55251_0    conda-forge

shunhuahan commented 8 months ago

Hi @Kiliankleemann,

Thanks for the update on your installation experiment! I will look into preparing a docker container with TELR and all required dependencies built in, might give you an update over the weekend.

Best, Shunhua

shunhuahan commented 8 months ago

Hi @Kiliankleemann,

I have prepared a docker container with TELR v1.1 and all its dependencies built-in. Here is an instruction on how to run TELR using this docker container. Could you please give it a try and see if it works for you? Thanks!

TELR Docker Image

This repository provides a Docker image to simplify the setup and execution of TELR without needing to deal with dependency issues.

Getting Started

1. Pull the Docker Image

To use TELR via Docker, first pull the Docker image from Docker Hub:

docker pull hanshunhua/telr_image:1.1

2. Run TELR using Docker

Given the various file inputs and optional arguments required by TELR, here's a general command structure to run TELR using the Docker image:

docker run -v /path/to/local/data:/data hanshunhua/telr_image:1.1 /bin/bash -c "source activate TELR && telr -i /data/READS -r /data/REFERENCE -l /data/LIBRARY -o /data/OUTPUT_DIR [other options]"

Replace /path/to/local/data with the path to your local directory containing the input files.
Replace READS, REFERENCE, LIBRARY with the actual input filenames.
Replace OUTPUT_DIR with the output directory name (under your local directory).
[other options] should be replaced with any other optional TELR arguments you want to use.

Sample Command:

Here is an example to run TELR through docker container using test input data available within the TELR repo. If the command works successfully, then you should expect to see the output files available under ~/git/TELR/test/test_output.

mkdir -p ~/git
cd ~/git
git clone git@github.com:bergmanlab/TELR.git
docker run -v ~/git/TELR/test:/data hanshunhua/telr_image:1.1 /bin/bash -c "source activate TELR && telr -i /data/reads.fasta -r /data/ref_38kb.fasta -l /data/library.fasta -o test_output"

TELR Options

Here's a quick overview of TELR's options:

Required Arguments:
- -i READS: Reads in fasta/fastq format or read alignments in bam format.
- -r REFERENCE: Reference genome in fasta format.
- -l LIBRARY: TE consensus sequences in fasta format.
Optional Arguments:
- Various options are available such as --aligner, --assembler, --polisher, --presets, --polish_iterations, and more. Please refer to TELR's official documentation or use the -h flag for a complete list and descriptions.

Troubleshooting and Support

If you encounter any issues using the TELR Docker image, please open an issue in the GitHub repository.

Kiliankleemann commented 8 months ago

I got the installation to work but also tried to docker now. Thank you so much for the efforts! I really appreciate it. For me it said that:

docker pull hanshunhua/telr_image:1.1
permission denied while trying to connect to the Docker daemon socket at unix:///var/run/docker.sock: Post "http://%2Fvar%2Frun%2Fdocker.sock/v1.24/images/create?fromImage=hanshunhua%2Ftelr_image&tag=1.1": dial unix /var/run/docker.sock: connect: permission denied

I will try on another machine.

shunhuahan commented 8 months ago

@Kiliankleemann thanks for helping me test this container!

There are two things that might result in the permission denied error.

Docker or the Daemon is not running.
Docker group has not been added to the user. You should either try to add docker to your user group (see https://www.digitalocean.com/community/questions/how-to-fix-docker-got-permission-denied-while-trying-to-connect-to-the-docker-daemon-socket) or just try sudo docker pull hanshunhua/telr_image:1.1 if you have sudo access.

Regardless, good to hear that the installation is working now (I'm assuming with conda/mamba).

Thanks, Shunhua

bergmanlab / TELR

Installation issue with conda #34

TELR Docker Image

Getting Started

1. Pull the Docker Image

2. Run TELR using Docker

Sample Command:

TELR Options

Troubleshooting and Support