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Lexogen-Tools / idemuxcpp

iDemux is an all-in-one command line tool that can be used for both demultiplexing and error correction of FASTQ files. It enables demultiplexing of i1 inline barcodes of Lexogen’s QuantSeq-Pool as well as demultiplexing of i7 and/or i5 indices of any other RNA-Seq library prep. iDemux can also be used for superior error correction of RNA-Seq libraries generated with Lexogen’s UDI 12 nt Unique Dual Indices. This C++ version is faster than the Python version but requires a certain proficiency in command line tool handling.
https://www.lexogen.com/indexing/12nt-dual-indexing-kits/
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barcodes path unavailable in conda install #1

Closed cachris1 closed 1 year ago

cachris1 commented 1 year ago

After installing with conda and running, I got this error: Error: the path /usr/share/idemuxcpp/barcodes/i1 is not available! It seems with conda the barcodes are by default located at:

~/miniconda3/envs/quantseq/share/idemuxcpp/

conda info:

     active environment : quantseq
    active env location : /home/cachris/miniconda3/envs/quantseq
            shell level : 2
       user config file : /home/cachris/.condarc
 populated config files :
          conda version : 23.3.1
    conda-build version : not installed
         python version : 3.10.11.final.0
       virtual packages : __archspec=1=x86_64
                          __glibc=2.35=0
                          __linux=5.15.0=0
                          __unix=0=0
       base environment : /home/cachris/miniconda3  (writable)
      conda av data dir : /home/cachris/miniconda3/etc/conda
  conda av metadata url : None
           channel URLs : https://repo.anaconda.com/pkgs/main/linux-64
                          https://repo.anaconda.com/pkgs/main/noarch
                          https://repo.anaconda.com/pkgs/r/linux-64
                          https://repo.anaconda.com/pkgs/r/noarch
          package cache : /home/cachris/miniconda3/pkgs
                          /home/cachris/.conda/pkgs
       envs directories : /home/cachris/miniconda3/envs
                          /home/cachris/.conda/envs
               platform : linux-64
             user-agent : conda/23.3.1 requests/2.28.1 CPython/3.10.11 Linux/5.15.0-71-generic ubuntu/22.04.1 glibc/2.35
                UID:GID : 1045:1079
             netrc file : None
           offline mode : False

conda list:


# packages in environment at /home/cachris/miniconda3/envs/quantseq:
#
# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
bamtools                  2.5.1               hd03093a_10    bioconda
bcrypt                    3.2.0            py36h7b6447c_0
blas                      1.0                         mkl
boost-cpp                 1.78.0               h6582d0a_3    conda-forge
brotlipy                  0.7.0           py36h27cfd23_1003
bzip2                     1.0.8                h7f98852_4    conda-forge
ca-certificates           2023.7.22            hbcca054_0    conda-forge
certifi                   2021.5.30        py36h06a4308_0
cffi                      1.14.6           py36h400218f_0
charset-normalizer        2.0.4              pyhd3eb1b0_0
cryptography              35.0.0           py36hd23ed53_0
dataclasses               0.8                pyh4f3eec9_6
dbus                      1.13.18              hb2f20db_0
docutils                  0.17.1           py36h06a4308_1
dropbox                   5.2.1                    py36_0    bioconda
expat                     2.4.9                h6a678d5_0
fastqc                    0.11.8                        0    bioconda
filechunkio               1.6                      py36_0    bioconda
freetype                  2.12.1               h4a9f257_0
ftputil                   3.2                      py36_0    bioconda
gdbm                      1.18                 hd4cb3f1_4
glib                      2.69.1               h4ff587b_1
icu                       72.1                 hcb278e6_0    conda-forge
idemux                    0.1.6              pyhdfd78af_0    bioconda
idemuxcpp                 0.1.9                h2d38e66_2    bioconda
idna                      3.3                pyhd3eb1b0_0
importlib_resources       5.2.0              pyhd3eb1b0_1
intel-openmp              2022.1.0          h9e868ea_3769
ld_impl_linux-64          2.38                 h1181459_1
libffi                    3.3                  he6710b0_2
libgcc-ng                 13.1.0               he5830b7_0    conda-forge
libgomp                   13.1.0               he5830b7_0    conda-forge
libpng                    1.6.39               h5eee18b_0
libsodium                 1.0.18               h7b6447c_0
libstdcxx-ng              13.1.0               hfd8a6a1_0    conda-forge
libxcb                    1.15                 h7f8727e_0
libzlib                   1.2.13               hd590300_5    conda-forge
mkl                       2020.2                      256
mkl-service               2.3.0            py36he8ac12f_0
mkl_fft                   1.3.0            py36h54f3939_0
mkl_random                1.1.1            py36h0573a6f_0
ncurses                   6.4                  h6a678d5_0
numpy                     1.19.2           py36h54aff64_0
numpy-base                1.19.2           py36hfa32c7d_0
openjdk                   11.0.13              h87a67e3_0
openssl                   1.1.1v               h7f8727e_0
pandas                    1.1.5            py36ha9443f7_0
paramiko                  2.8.1              pyhd3eb1b0_0
pcre                      8.45                 h295c915_0
perl                      5.34.0               h5eee18b_2
pip                       21.2.2           py36h06a4308_0
psutil                    5.8.0            py36h27cfd23_1
pycparser                 2.21               pyhd3eb1b0_0
pynacl                    1.4.0            py36h7b6447c_1
pyopenssl                 22.0.0             pyhd3eb1b0_0
pysftp                    0.2.9                    py36_0    bioconda
pysocks                   1.7.1            py36h06a4308_0
python                    3.6.13               h12debd9_1
python-dateutil           2.8.2              pyhd3eb1b0_0
pytz                      2021.3             pyhd3eb1b0_0
pyyaml                    5.4.1            py36h27cfd23_1
readline                  8.2                  h5eee18b_0
requests                  2.27.1             pyhd3eb1b0_0
setuptools                58.0.4           py36h06a4308_0
six                       1.16.0             pyhd3eb1b0_1
snakemake                 3.13.3                   py36_0    bioconda
sqlite                    3.41.2               h5eee18b_0
tk                        8.6.12               h1ccaba5_0
tqdm                      4.7.2                    py36_0    bioconda
urllib3                   1.26.8             pyhd3eb1b0_0
wheel                     0.37.1             pyhd3eb1b0_0
wrapt                     1.12.1           py36h7b6447c_1
xz                        5.2.6                h166bdaf_0    conda-forge
yaml                      0.2.5                h7b6447c_0
zipp                      3.6.0              pyhd3eb1b0_0
zlib                      1.2.13               hd590300_5    conda-forge
zstd                      1.5.2                hfc55251_7    conda-forge
entzian commented 1 year ago

Dear @cachris1, thanks for opening this issue! We will improve loading the barcode maps in the next version. In the current version, you can use the command line parameter -m, --correction-map-prefix=STRING or in your case -m ~/miniconda3/envs/quantseq/share/idemuxcpp/barcodes . In general the barcodes main directory can be found with find / -wholename "*idemuxcpp/barcodes" -type d.

cachris1 commented 1 year ago

Thanks for the reply, I will try that out.