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KatyBrown / CIAlign

MIT License
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Update conda CIAlign to latest version? #54

Closed bioteksampath closed 6 months ago

bioteksampath commented 1 year ago

Hi, I'm just wondering, if you could help update the latest version of CIAlign through conda. The version in Conda is old ( v1.0.18) and seems missing few flags (--crop_divergent).

Thanks 

(uTE2_annot) [sap223@cnic-base-lgn-19002 test_sam]$ CIAlign -v
1.0.18
uTE2_annot) [sap223@cnic-base-lgn-19002 test_sam]$ CIAlign --infile put_Ltr1.maf --crop_divergent
usage: CIAlign [--infile INFILE] [--inifile INIFILE]
               [--outfile_stem OUTFILE_STEM] [--all] [--clean] [--visualise]
               [--interpret] [--silent] [--crop_ends]
               [--crop_ends_mingap_perc float, 0..0.5)]
               [--crop_ends_redefine_perc (float, 0..0.5)]
               [--remove_divergent] [--remove_divergent_minperc (float, 0..1)]
               [--remove_insertions] [--insertion_min_size (int, 1..n_col)]
               [--insertion_max_size (int, 1..1000)]
               [--insertion_min_flank (int, 0..n_col/2)]
               [--insertion_min_perc (float, 0..1)] [--remove_short]
               [--remove_min_length (int, 0..n_col] [--keep_gaponly]
               [--make_consensus] [--consensus_type CONSENSUS_TYPE]
               [--consensus_keep_gaps] [--consensus_name CONSENSUS_NAME]
               [--plot_input] [--plot_output] [--plot_markup]
               [--plot_dpi PLOT_DPI] [--plot_format PLOT_FORMAT]
               [--plot_width PLOT_WIDTH] [--plot_height PLOT_HEIGHT]
               [--plot_keep_numbers] [--plot_force_numbers]
               [--make_sequence_logo]
               [--sequence_logo_type SEQUENCE_LOGO_TYPE]
               [--sequence_logo_dpi SEQUENCE_LOGO_DPI]
               [--sequence_logo_font SEQUENCE_LOGO_FONT]
               [--sequence_logo_nt_per_row SEQUENCE_LOGO_NT_PER_ROW]
               [--sequence_logo_filetype SEQUENCE_LOGO_FILETYPE]
               [--logo_start LOGO_START] [--logo_end LOGO_END]
               [--list_fonts_only] [--plot_coverage_input]
               [--plot_coverage_output]
               [--plot_coverage_dpi PLOT_COVERAGE_DPI]
               [--plot_coverage_height PLOT_COVERAGE_HEIGHT]
               [--plot_coverage_width PLOT_COVERAGE_WIDTH]
               [--plot_coverage_colour PLOT_COVERAGE_COLOUR]
               [--plot_coverage_filetype PLOT_COVERAGE_FILETYPE]
               [--make_similarity_matrix_input]
               [--make_similarity_matrix_output]
               [--make_simmatrix_dp MAKE_SIMMATRIX_DP]
               [--make_simmatrix_minoverlap MAKE_SIMMATRIX_MINOVERLAP]
               [--make_simmatrix_keepgaps MAKE_SIMMATRIX_KEEPGAPS]
               [--unalign_input] [--unalign_output] [--replace_input]
               [--replace_output] [-h] [-v]
CIAlign: error: unrecognized arguments: --crop_divergent
KatyBrown commented 6 months ago

I realise it's been almost a year, sorry, but just to let you know the conda version of CIAlign is now the current version.