install error

[zhoudreames]

following your installation, I got the error in this step:"conda build conda-recipe -c conda-forge";
this is my error:

I don't know why, Is there any other way to install the software quickly？
In addition, I want to filter the CIGAR with N >10000 in RNA bam files, if there are no other methods to install this software, can you provide some simple code to achieve it？Thank~

this my bam file， of which the reads "9ae8a1cd-1a71-40d1-ab06-f1567ec79f9a" contained 1593N，I want to exclude it.

Dreames

[zhoudreames]

@GDelevoye I am so sorry to disturb you， can you help me? Thanks~

[GDelevoye]

I think I will need some time to debug the conda package, but if you can't wait maybe you can use this minimal example ?

EDIT: Note that in the screenshot you gave me, your .bam file does not seem to have all fields. If you have <= 5 fields, you may have a segmentation fault (core dumped) error. Make sure your .bam file is correct because my code doesn't check that it is correct; it just assumes it

EDIT : If you need to make more advanced operations you can still check this wiki page. All the "filter" functions that I wrote there remain basically valid

[GDelevoye]

The previous minimal example should do exactly what you want. However if you want, you can help me debugging what has gone wrong with the conda install. Sometimes it's just conda being completely stupid

This solution worked like a charm for me (and should in theory work in Ubuntu or MacOS), please let me know if you have any trouble with it :

Install mamba

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

Once it is done, Restart the terminal

If you don't do it, you'll have problems

Build and install the package with mamba instead of conda

Ensure that you are using mamba instead of conda, and then :

git clone https://github.com/GDelevoye/cigarfilter/
cd cigarfilter
mamba create -n cf cxx-compiler cmake make pip "conan<2" boa -c conda-forge
mamba actvate cf
conda mambabuild ./conda-recipe/ -c conda-forge
mamba install -c local cigarfilter

Test that everything works

Make sure that you are using the "cf" mamba environment that was created in the previous script

(base) delevoye@Dell-G15-5530:~/cigarfilter$ mamba activate cf
(cf) delevoye@Dell-G15-5530:~/cigarfilter$ cigarfilter -h
USAGE:
  cigarfilter [-?|-h|--help] [-f|--filter <filter name>] [-p|--print_header <bool>]

Display usage information.

OPTIONS, ARGUMENTS:
  -?, -h, --help          
  -f, --filter <filter name>
                          Use "cigarfilter_config help" for more info.
  -p, --print_header <bool>
                          When set to false, the header is not printed. <default: TRUE>

(cf) delevoye@Dell-G15-5530:~/cigarfilter$ cigarfilter_config -h
  * help :
	 Displays this help

  * pluginpath :
	 Displays the path were filters are stored. Manually modify them only at your own risks.

  * list :
	 Lists all available filters.

  * add :
	 Adds a filter from a .cpp file (see README online at https://github.com/GDelevoye/cigarfilter).

  * remove :
	 Removes a filter. Example : "cigarfilter_config remove default".

  * clean :
	 Cleans all logs and temporary files.

  * purge :
	 Cleans all logs, temporary files and all filters except the default one.

(cf) delevoye@Dell-G15-5530:~/cigarfilter$ cigarfilter_test
Running main() from /home/delevoye/.conan/data/gtest/1.12.1/_/_/build/bd0690086619c54f81a8365940843110bf637ce7/src/googletest/src/gtest_main.cc
[==========] Running 20 tests from 3 test suites.
[----------] Global test environment set-up.
[----------] 12 tests from cigar
[ RUN      ] cigar.t_listdigit
[       OK ] cigar.t_listdigit (0 ms)
[ RUN      ] cigar.t_eq
[       OK ] cigar.t_eq (0 ms)
[ RUN      ] cigar.t_empty
[       OK ] cigar.t_empty (0 ms)
[ RUN      ] cigar.t_S
[       OK ] cigar.t_S (0 ms)
[ RUN      ] cigar.t_D
[       OK ] cigar.t_D (0 ms)
[ RUN      ] cigar.t_I
[       OK ] cigar.t_I (0 ms)
[ RUN      ] cigar.t_X
[       OK ] cigar.t_X (0 ms)
[ RUN      ] cigar.t_N
[       OK ] cigar.t_N (0 ms)
[ RUN      ] cigar.t_P
[       OK ] cigar.t_P (0 ms)
[ RUN      ] cigar.t_H
[       OK ] cigar.t_H (0 ms)
[ RUN      ] cigar.t_M
[       OK ] cigar.t_M (0 ms)
[ RUN      ] cigar.complex_1
[       OK ] cigar.complex_1 (0 ms)
[----------] 12 tests from cigar (0 ms total)

[----------] 2 tests from plugin_helpers
[ RUN      ] plugin_helpers.plugindir
[       OK ] plugin_helpers.plugindir (16 ms)
[ RUN      ] plugin_helpers.get_default_plugin
[       OK ] plugin_helpers.get_default_plugin (17 ms)
[----------] 2 tests from plugin_helpers (33 ms total)

[----------] 6 tests from ExampleTest
[ RUN      ] ExampleTest.iterate_groups_t
[       OK ] ExampleTest.iterate_groups_t (51 ms)
[ RUN      ] ExampleTest.default_t
[       OK ] ExampleTest.default_t (51 ms)
[ RUN      ] ExampleTest.example1_t
[       OK ] ExampleTest.example1_t (50 ms)
[ RUN      ] ExampleTest.example2_t
[       OK ] ExampleTest.example2_t (50 ms)
[ RUN      ] ExampleTest.example3_t
[       OK ] ExampleTest.example3_t (51 ms)
[ RUN      ] ExampleTest.example4_t
ERROR : Could not remove the tmp file in fixture "StdoutFixture"
[       OK ] ExampleTest.example4_t (16 ms)
[----------] 6 tests from ExampleTest (272 ms total)

[----------] Global test environment tear-down
[==========] 20 tests from 3 test suites ran. (306 ms total)
[  PASSED  ] 20 tests.

[zhoudreames]

The previous minimal example should do exactly what you want. However if you want, you can help me debugging what has gone wrong with the conda install. Sometimes it's just conda being completely stupid

This solution worked like a charm for me (and should in theory work in Ubuntu or MacOS), please let me know if you have any trouble with it :

Install mamba

wget "https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-$(uname)-$(uname -m).sh"
bash Miniforge3-$(uname)-$(uname -m).sh

Once it is done, Restart the terminal

If you don't do it, you'll have problems

Build and install the package with mamba instead of conda

Ensure that you are using mamba instead of conda, and then :

git clone https://github.com/GDelevoye/cigarfilter/
cd cigarfilter
mamba create -n cf cxx-compiler cmake make pip "conan<2" boa -c conda-forge
mamba actvate cf
conda mambabuild ./conda-recipe/ -c conda-forge
mamba install -c local cigarfilter

Test that everything works

Make sure that you are using the "cf" mamba environment that was created in the previous script

(base) delevoye@Dell-G15-5530:~/cigarfilter$ mamba activate cf
(cf) delevoye@Dell-G15-5530:~/cigarfilter$ cigarfilter -h
USAGE:
  cigarfilter [-?|-h|--help] [-f|--filter <filter name>] [-p|--print_header <bool>]

Display usage information.

OPTIONS, ARGUMENTS:
  -?, -h, --help          
  -f, --filter <filter name>
                          Use "cigarfilter_config help" for more info.
  -p, --print_header <bool>
                          When set to false, the header is not printed. <default: TRUE>

(cf) delevoye@Dell-G15-5530:~/cigarfilter$ cigarfilter_config -h
  * help :
	 Displays this help

  * pluginpath :
	 Displays the path were filters are stored. Manually modify them only at your own risks.

  * list :
	 Lists all available filters.

  * add :
	 Adds a filter from a .cpp file (see README online at https://github.com/GDelevoye/cigarfilter).

  * remove :
	 Removes a filter. Example : "cigarfilter_config remove default".

  * clean :
	 Cleans all logs and temporary files.

  * purge :
	 Cleans all logs, temporary files and all filters except the default one.

(cf) delevoye@Dell-G15-5530:~/cigarfilter$ cigarfilter_test
Running main() from /home/delevoye/.conan/data/gtest/1.12.1/_/_/build/bd0690086619c54f81a8365940843110bf637ce7/src/googletest/src/gtest_main.cc
[==========] Running 20 tests from 3 test suites.
[----------] Global test environment set-up.
[----------] 12 tests from cigar
[ RUN      ] cigar.t_listdigit
[       OK ] cigar.t_listdigit (0 ms)
[ RUN      ] cigar.t_eq
[       OK ] cigar.t_eq (0 ms)
[ RUN      ] cigar.t_empty
[       OK ] cigar.t_empty (0 ms)
[ RUN      ] cigar.t_S
[       OK ] cigar.t_S (0 ms)
[ RUN      ] cigar.t_D
[       OK ] cigar.t_D (0 ms)
[ RUN      ] cigar.t_I
[       OK ] cigar.t_I (0 ms)
[ RUN      ] cigar.t_X
[       OK ] cigar.t_X (0 ms)
[ RUN      ] cigar.t_N
[       OK ] cigar.t_N (0 ms)
[ RUN      ] cigar.t_P
[       OK ] cigar.t_P (0 ms)
[ RUN      ] cigar.t_H
[       OK ] cigar.t_H (0 ms)
[ RUN      ] cigar.t_M
[       OK ] cigar.t_M (0 ms)
[ RUN      ] cigar.complex_1
[       OK ] cigar.complex_1 (0 ms)
[----------] 12 tests from cigar (0 ms total)

[----------] 2 tests from plugin_helpers
[ RUN      ] plugin_helpers.plugindir
[       OK ] plugin_helpers.plugindir (16 ms)
[ RUN      ] plugin_helpers.get_default_plugin
[       OK ] plugin_helpers.get_default_plugin (17 ms)
[----------] 2 tests from plugin_helpers (33 ms total)

[----------] 6 tests from ExampleTest
[ RUN      ] ExampleTest.iterate_groups_t
[       OK ] ExampleTest.iterate_groups_t (51 ms)
[ RUN      ] ExampleTest.default_t
[       OK ] ExampleTest.default_t (51 ms)
[ RUN      ] ExampleTest.example1_t
[       OK ] ExampleTest.example1_t (50 ms)
[ RUN      ] ExampleTest.example2_t
[       OK ] ExampleTest.example2_t (50 ms)
[ RUN      ] ExampleTest.example3_t
[       OK ] ExampleTest.example3_t (51 ms)
[ RUN      ] ExampleTest.example4_t
ERROR : Could not remove the tmp file in fixture "StdoutFixture"
[       OK ] ExampleTest.example4_t (16 ms)
[----------] 6 tests from ExampleTest (272 ms total)

[----------] Global test environment tear-down
[==========] 20 tests from 3 test suites ran. (306 ms total)
[  PASSED  ] 20 tests.

Thank you for the detailed replay, I try it.