cDNA_Cupcake is painfuly to install, just get rid of it.

[diekhans]

Is there an existing issue for this?

• I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

• I have loaded the SQANTI3.env conda environment

Problem description

Even with the updated version of cDNA_Cupcake, one collaborator was getting the error:

Cythonizing cupcake/tofu/branch/c_branch.pyx
  Error compiling Cython file:

while I was able to install it. The difference appears to be issues with the conda install, so time to. remove conda and reinstall it all.

But why do faithful SQANTI3 fans have to suffer installing cDNA_Cupcake when SQUANTI3 uses a tiny faction of Cupcake?

How about just copying the files that SQANT3 uses, convert them to Python3 and be done with this pain?

Please!

Code sample

No response

Error

No response

Anything else?

No response

[francicco]

I'm also having a hard time:

(SQANTI3.env) [tk19812@bp1-login01 cDNA_Cupcake]$ python setup.py build
Compiling cupcake/tofu/branch/intersection_unique.pyx because it changed.
Compiling cupcake/tofu/branch/c_branch.pyx because it changed.
Compiling cupcake/ice/find_ECE.pyx because it changed.
[1/3] Cythonizing cupcake/ice/find_ECE.pyx
[2/3] Cythonizing cupcake/tofu/branch/c_branch.pyx
[3/3] Cythonizing cupcake/tofu/branch/intersection_unique.pyx
running build
running build_py
creating build
creating build/lib.linux-x86_64-2.7
creating build/lib.linux-x86_64-2.7/cupcake
copying cupcake/__init__.py -> build/lib.linux-x86_64-2.7/cupcake
creating build/lib.linux-x86_64-2.7/cupcake/io
copying cupcake/io/BioReaders.py -> build/lib.linux-x86_64-2.7/cupcake/io
copying cupcake/io/GFF.py -> build/lib.linux-x86_64-2.7/cupcake/io
copying cupcake/io/__init__.py -> build/lib.linux-x86_64-2.7/cupcake/io
copying cupcake/io/SeqReaders.py -> build/lib.linux-x86_64-2.7/cupcake/io
copying cupcake/io/BED.py -> build/lib.linux-x86_64-2.7/cupcake/io
creating build/lib.linux-x86_64-2.7/cupcake/ice
copying cupcake/ice/setup2.py -> build/lib.linux-x86_64-2.7/cupcake/ice
copying cupcake/ice/ice_align_core.py -> build/lib.linux-x86_64-2.7/cupcake/ice
copying cupcake/ice/__init__.py -> build/lib.linux-x86_64-2.7/cupcake/ice
creating build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/color_bed12_post_sqanti.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/get_counts_by_barcode.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/collapse_isoforms_by_sam.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/get_abundance_post_collapse.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/fusion_finder.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/filter_monoexon.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/__init__.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/utils.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/filter_by_count.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/filter_away_subset.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/fusion_collate_info.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/compare_junctions.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
copying cupcake/tofu/simple_stats_post_collapse.py -> build/lib.linux-x86_64-2.7/cupcake/tofu
creating build/lib.linux-x86_64-2.7/cupcake/tofu/branch
copying cupcake/tofu/branch/branch_simple2.py -> build/lib.linux-x86_64-2.7/cupcake/tofu/branch
copying cupcake/tofu/branch/setup2.py -> build/lib.linux-x86_64-2.7/cupcake/tofu/branch
copying cupcake/tofu/branch/__init__.py -> build/lib.linux-x86_64-2.7/cupcake/tofu/branch
creating build/lib.linux-x86_64-2.7/cupcake/tofu/counting
copying cupcake/tofu/counting/combine_abundance_across_samples.py -> build/lib.linux-x86_64-2.7/cupcake/tofu/counting
copying cupcake/tofu/counting/summarize_sample_GFF_junctions.py -> build/lib.linux-x86_64-2.7/cupcake/tofu/counting
copying cupcake/tofu/counting/__init__.py -> build/lib.linux-x86_64-2.7/cupcake/tofu/counting
copying cupcake/tofu/counting/chain_fusion_samples.py -> build/lib.linux-x86_64-2.7/cupcake/tofu/counting
copying cupcake/tofu/counting/scrub_sample_GFF_junctions.py -> build/lib.linux-x86_64-2.7/cupcake/tofu/counting
copying cupcake/tofu/counting/chain_samples.py -> build/lib.linux-x86_64-2.7/cupcake/tofu/counting
creating build/lib.linux-x86_64-2.7/phasing
copying phasing/snps_to_vcf.py -> build/lib.linux-x86_64-2.7/phasing
copying phasing/simulate_phasing_data_from_fasta.py -> build/lib.linux-x86_64-2.7/phasing
copying phasing/run_phaser.py -> build/lib.linux-x86_64-2.7/phasing
copying phasing/__init__.py -> build/lib.linux-x86_64-2.7/phasing
copying phasing/mag_phaser.py -> build/lib.linux-x86_64-2.7/phasing
copying phasing/create_fake_genome.py -> build/lib.linux-x86_64-2.7/phasing
creating build/lib.linux-x86_64-2.7/phasing/io
copying phasing/io/VariantPhaseCleaner.py -> build/lib.linux-x86_64-2.7/phasing/io
copying phasing/io/MPileUpVariantCaller.py -> build/lib.linux-x86_64-2.7/phasing/io
copying phasing/io/coordinate_mapper.py -> build/lib.linux-x86_64-2.7/phasing/io
copying phasing/io/VariantPhaser.py -> build/lib.linux-x86_64-2.7/phasing/io
copying phasing/io/SAMMPileUpReader.py -> build/lib.linux-x86_64-2.7/phasing/io
copying phasing/io/__init__.py -> build/lib.linux-x86_64-2.7/phasing/io
copying phasing/io/MummerSNPReader.py -> build/lib.linux-x86_64-2.7/phasing/io
running build_ext
building 'cupcake.tofu.branch.intersection_unique' extension
creating build/temp.linux-x86_64-2.7
creating build/temp.linux-x86_64-2.7/cupcake
creating build/temp.linux-x86_64-2.7/cupcake/tofu
creating build/temp.linux-x86_64-2.7/cupcake/tofu/branch
/user/work/tk19812/scWorkshop/miniforge3/envs/SQANTI3.env/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O3 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /user/work/tk19812/scWorkshop/miniforge3/envs/SQANTI3.env/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /user/work/tk19812/scWorkshop/miniforge3/envs/SQANTI3.env/include -fPIC -I/user/home/tk19812/.local/lib/python2.7/site-packages/numpy/core/include -I/user/work/tk19812/scWorkshop/miniforge3/envs/SQANTI3.env/include/python2.7 -c cupcake/tofu/branch/intersection_unique.c -o build/temp.linux-x86_64-2.7/cupcake/tofu/branch/intersection_unique.o
In file included from cupcake/tofu/branch/intersection_unique.c:19:
/user/work/tk19812/scWorkshop/miniforge3/envs/SQANTI3.env/include/python2.7/Python.h:47:10: fatal error: crypt.h: No such file or directory
   47 | #include <crypt.h>
      |          ^~~~~~~~~
compilation terminated.
error: command '/user/work/tk19812/scWorkshop/miniforge3/envs/SQANTI3.env/bin/x86_64-conda-linux-gnu-cc' failed with exit status 1

[carolinamonzo]

This issue was solved by @diekhans and @TianYuan-Liu in the new release of SQANTI3 v5.2.1, where cDNA_cupcake is no longer a dependency.

[francicco]

Great! I reinstalled everything from scratch and it looks like it almost works.

I think there's something going on with the R scripts tho...
Cheers
F

(SQANTI3.env) [tk19812@bp1-login01 SQANTI3-5.2.1]$ ./run_SQANTI3_rules_filter.sh 
Rscript (R) version 4.3.1 (2023-06-16)
Write arguments to /user/work/tk19812/software/SQANTI3-5.2.1/example/rules_filter_output/UHR_chr22_params.txt...

Running SQANTI3 filtering...

/user/work/tk19812/scWorkshop/miniforge3/envs/SQANTI3.env/bin/Rscript /user/work/tk19812/software/SQANTI3-5.2.1/utilities/filter/SQANTI3_rules_filter.R -c /user/work/tk19812/software/SQANTI3-5.2.1/example/SQANTI3_QC_output/UHR_chr22_classification.txt -o UHR_chr22 -d example/rules_filter_output/ -j /user/work/tk19812/software/SQANTI3-5.2.1/utilities/filter/filter_default.json -u /user/work/tk19812/software/SQANTI3-5.2.1/utilities -e False
Warning message:
package ‘optparse’ was built under R version 4.3.2 
Warning message:
package ‘jsonlite’ was built under R version 4.3.2 

Attaching package: ‘dplyr’

The following objects are masked from ‘package:stats’:

    filter, lag

The following objects are masked from ‘package:base’:

    intersect, setdiff, setequal, union

Warning message:
package ‘dplyr’ was built under R version 4.3.2 
-------------------------------------------------

 	 Reading classification file

--------------------------------------------------
-------------------------------------------------

 	 Reading JSON file with rules to filter

--------------------------------------------------
-------------------------------------------------

 	 Performing filtering

--------------------------------------------------
-------------------------------------------------

 	 Writting results

--------------------------------------------------

-------------------------------------------------

 	 SQANTI3 Rules filter report

--------------------------------------------------
Loading required package: magrittr

Reading Rules result classification table...
Warning message:
There were 2 warnings in `dplyr::mutate()`.
The first warning was:
ℹ In argument: `structural_category = `%>%`(...)`.
Caused by warning:
! Unknown levels in `f`: genic_intron
ℹ Run `dplyr::last_dplyr_warnings()` to see the 1 remaining warning. 
Loading required package: ggplot2
Warning message:
package ‘ggplot2’ was built under R version 4.3.2 
Error in contrib.url(repos, type) : 
  trying to use CRAN without setting a mirror
Calls: suppressMessages ... withCallingHandlers -> install.packages -> startsWith -> contrib.url
Execution halted