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If you are wondering where the data of this site comes from, please visit https://api.github.com/users/luispedro/events. GitMemory does not store any data, but only uses NGINX to cache data for a period of time. The idea behind GitMemory is simply to give users a better reading experience.
Luis Pedro Coelho luispedro Fudan University Luxembourg & Shanghai http://luispedro.org

greenelab/covid19-review 112

A collaborative review of the emerging COVID-19 literature. Join the chat here:

BigDataBiology/macrel 24

Predict AMPs in (meta)genomes and peptides

luispedro/android-fuse 4

Mount an android device using FUSE

luispedro/base-user 2

dot files and the like so that I can set up a new computer with a couple of command line calls

luispedro/beiraproject 2

Beira Project Stuff

luispedro/alist 1

Append List in Haskell

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Luis Pedro Coelho

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ENH Update publication list

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Luis Pedro Coelho

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Luis Pedro Coelho

commit sha fbe97f1904bf5990cdfc24cd74f85c15e0751818

ENH Update elm versions The newer elm is slightly stricter with Module names as well

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Luis Pedro Coelho

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ENH Update lab manual - Information on getting a computer - Mention end-of-semester meetings

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Luis Pedro Coelho

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ENH Update macrel website - Point to PeerJ

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Celio Santos-Jr

commit sha 42c77622510be1e023c5bbd8a052e1632d6f4068

add mamba to install dependencies and environment (#45) * alter the install tool conda --> mamba * DOC update * update actions with mamba

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Celio Santos-Jr

commit sha 71aec37e5e234666046d31d7877a034748267253

alter the install procedures -- add mamba

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Luis Pedro Coelho

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ENH Turn assert into warnings

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Luis Pedro Coelho

commit sha d3b9b8538fabfe9ffb7c664dcc62cfa325c1b3d9

MIN Defensive programming

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Luis Pedro Coelho

commit sha 061ce4c045aa0614f09ac2029d7afe6dbcd08f56

ENH Normalize tet genes too

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Luis Pedro Coelho

commit sha d845173112de6ddb939d7d73f7f6520f7529f3a2

MIN Add deprecation note

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Luis Pedro Coelho

commit sha b2f9f54397117dd8d42702daf7635a380dee4113

DOC+MIN Add links to docs & paper

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Luis Pedro Coelho

commit sha b9e37df92d814fb43968d73d6e8d97be2e580ab8

MIN Create the output directory

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Luis Pedro Coelho

commit sha d70107bf60414b8f552bc1c3fd4b85fca53c832d

BUG Match output name to .gitignore

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Luis Pedro Coelho

commit sha 2206ce368f982e3269c70ad7305274acafe43238

DOC Show how to build a conda environment

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Luis Pedro Coelho

commit sha c976c3afbe06fa3940bea31b99d2725b214e2613

BUG Fix classifier list in setup.py - "Programming Language :: R :: 3.6" is not part of the PyPI list - Update status to stable

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Celio Santos-Jr

commit sha 9abe91d2795832056c0cb8204419e7e2166bfec2

BUG Fix single-ended abundance mode abundance and reads modes were broken for single-ended reads (Cherry-picked from main branch)

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Luis Pedro Coelho

commit sha 86be28ca9f1474da4b254bcae9d79e66307e258f

RFCT Use os.makedirs This function has been in Python with the exist_ok argument since 3.3, so the old reimplementation is no longer needed.

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issue commentBigDataBiology/SemiBin

Problems with contig names

The line

    sample_name, contig_name = seq_record.id.split(separator)

should probably be

    sample_name, contig_name = seq_record.id.split(separator, 1)

because, otherwise, it can lead to issues if the contig name also contains the separator (not likely with :, but not unlikely with _).

For UX reasons, I might even add:

    if separator not in seq_record.id:
       raise ValueError(f"Expected contigs to contain separator character ({separator}), found {seq_record.id}")
    sample_name, contig_name = seq_record.id.split(separator, 1)
SilasK

comment created time in 11 days

issue commentconda-forge/ghc-feedstock

GHC looks for paths in the build environment (which do not exist when it is running)

Yes. This is still happening.

conda create -n ghc-test
conda activate ghc-test
conda install -c conda-forge ghc

ghc-pkg recache
ghc Hello.hs -o hello

returns an error:


[1 of 1] Compiling Main             ( Hello.hs, Hello.o )

<no location info>: error:
    Warning: Couldn't figure out C compiler information!
             Make sure you're using GNU gcc, or clang
ghc: could not execute: /home/conda/feedstock_root/build_artifacts/ghc_1631487753784/_build_env/bin/x86_64-conda-linux-gnu-gcc

The file Hello.hs is very simple:

module Main where

main = putStrLn "Hello World"

Again, the /home/luispedro/.anaconda/envs/ghc-test/lib/ghc-8.10.4/settings file references these paths:

[("GCC extra via C opts", "")
,("C compiler command", "/home/conda/feedstock_root/build_artifacts/ghc_1631487753784/_build_env/bin/x86_64-conda-linux-gnu-gcc")
,("C compiler flags", "")
,("C++ compiler flags", "")
,("C compiler link flags", "")
,("C compiler supports -no-pie", "YES")
,("Haskell CPP command", "/home/conda/feedstock_root/build_artifacts/ghc_1631487753784/_build_env/bin/x86_64-conda-linux-gnu-gcc")
,("Haskell CPP flags", "-E -undef -traditional")
,("ld command", "/home/conda/feedstock_root/build_artifacts/ghc_1631487753784/_build_env/bin/x86_64-conda-linux-gnu-ld")
,("ld flags", "")
,("ld supports compact unwind", "NO")
,("ld supports build-id", "YES")
,("ld supports filelist", "NO")
,("ld is GNU ld", "YES")
,("Merge objects command", "/home/conda/feedstock_root/build_artifacts/ghc_1631487753784/_build_env/bin/x86_64-conda-linux-gnu-ld")
,("Merge objects flags", "-r")
,("ar command", "x86_64-unknown-linux-gnu-ar")
,("ar flags", "q")
,("ar supports at file", "YES")
,("ranlib command", "/home/conda/feedstock_root/build_artifacts/ghc_1631487753784/_build_env/bin/x86_64-conda-linux-gnu-ranlib")
,("otool command", "otool")
,("install_name_tool command", "install_name_tool")
,("touch command", "touch")
,("dllwrap command", "/bin/false")
,("windres command", "/bin/false")
,("libtool command", "libtool")
,("unlit command", "$topdir/bin/unlit")
,("cross compiling", "NO")
,("target platform string", "x86_64-unknown-linux")
,("target os", "OSLinux")
,("target arch", "ArchX86_64")
,("target word size", "8")
,("target has GNU nonexec stack", "YES")
,("target has .ident directive", "YES")
,("target has subsections via symbols", "NO")
,("target has RTS linker", "YES")
,("Unregisterised", "NO")
,("LLVM target", "x86_64-unknown-linux")
,("LLVM llc command", "llc")
,("LLVM opt command", "opt")
,("LLVM clang command", "clang")
,("integer library", "integer-gmp")
,("Use interpreter", "YES")
,("Use native code generator", "YES")
,("Support SMP", "YES")
,("RTS ways", "l debug thr thr_debug thr_l thr_p dyn debug_dyn thr_dyn thr_debug_dyn l_dyn thr_l_dyn thr_debug_p debug_p")
,("Tables next to code", "YES")
,("Leading underscore", "NO")
,("Use LibFFI", "NO")
,("Use Threads", "YES")
,("Use Debugging", "NO")
,("RTS expects libdw", "NO")
]
luispedro

comment created time in 13 days

issue commentBigDataBiology/SemiBin

Problems with contig names

@SilasK : Often the samples all have similarly named contigs (if they are the output of an assembler, it'll be something like k141_123 or something) and we cannot assume that they will be unique. This is why the interface is how it is. I do confess that when @psj1997 first implemented this, I also thought it was confusing, but I frankly have no better idea on how to do it in a general way.

I think that introducing a subcommand to generate the combined FASTA file in the right way is a good idea and could avoid some UX issues. The command can use : by default, but also check that there are no naming conflicts, &c.

Additionally, it could create an NGLess script for further processing (while leaving the option of using other tools open for more advanced users).

SilasK

comment created time in 13 days

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psj1997

commit sha b3492f69002dd5517c47220092986ccdcb11d38f

Remove --input-bam in train and bin subcommand

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psj1997

commit sha f3fa84437692ee38f2176645796962f038317c9a

BUG Fix testing

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psj1997

commit sha f2cfffe9e6c81d11ce3fae003d809f937134ce21

Bug Fix testing

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psj1997

commit sha c753907fb4142cc3a033dcbed709516c49789a56

Bug Fix testing

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psj1997

commit sha bbe17167feddcfe923fe11bed4406ae9daf02761

Bug Fix testing

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psj1997

commit sha 5f725ddf9f9ca30addaaa97eca44744fd8530bff

BUG Fix args validation

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issue commentBigDataBiology/SemiBin

Enhancement:

This is a good point. We did pick one specific version as default, but in principle, any version of GTDB would work well for SemiBin (@psj1997, right?).

Maybe this needs to be clearer in the docs.

SilasK

comment created time in 14 days

issue commentluispedro/mahotas

"Input data has unexpected types" - Bug in mahotas.features.lbp.lbp

Can you perhaps post the image?

What is the dtype (i.e., print(image.dtype)))?

fateh288

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Celio Santos-Jr

commit sha 324b31bd6d0ac83b746aacb8f93eeaab71a8778b

BUG Fix single-ended abundance mode abundance and reads modes were broken for single-ended reads

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Celio Santos-Jr

commit sha 324b31bd6d0ac83b746aacb8f93eeaab71a8778b

BUG Fix single-ended abundance mode abundance and reads modes were broken for single-ended reads

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Celio Santos-Jr

commit sha 6948db8237fbd6e4129d42907e703c76e8bc0e46

BUG Fix single-ended abundance mode abundance and reads modes were broken for single-ended reads

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Celio Santos-Jr

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BUG Fix single-ended abundance mode abundance and reads modes were broken for single-ended reads

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Luis Pedro Coelho

commit sha c22df9187795b7c3c92635b7f97af9d91e844c5f

BUG Fix classifier list in setup.py - "Programming Language :: R :: 3.6" is not part of the PyPI list - Update status to stable

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Luis Pedro Coelho

commit sha 9cffa2ac9be0821705165d967fe5a3a3c8c286dd

ENH Handle .bz2 and .xz compressed FASTA files

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Luis Pedro Coelho

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DOC Another FAQ: isolate genome support

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