profile
viewpoint

daissi/bashtop 0

Linux/OSX/FreeBSD resource monitor

daissi/bioconda-recipes 0

Conda recipes for the bioconda channel.

daissi/bowtie 0

An ultrafast memory-efficient short read aligner

daissi/fastp 0

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting...)

daissi/GEMMA 0

Genome-wide Efficient Mixed Model Association

daissi/gnm 0

gnm package for generalized nonlinear models in R

daissi/isoband 0

isoband: An R package to generate contour lines and polygons.

daissi/libmtp 0

A library to access MTP (Media Transfer Protocol) Devices.

daissi/libofx 0

The libofx OFX banking protocol abstraction library

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 9e15f8b7b8c1ead7ded555a8a927fd079a7dc027

Check for presence of STOP in phase

view details

push time in 4 days

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 3831884059ef6b9d06ec7e8b027ac949614bc5d8

Homogenize print output

view details

push time in 4 days

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 8db6cf9ae6779d0dbde1ef8dd1ae1180f7cc6100

Homogenize print output

view details

push time in 4 days

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 709c313401b0694e31f16196d6b91bb9ff2da8ea

Fix my_transcript_id for GRCh 38

view details

push time in 6 days

issue openedjeroen/commonmark

CVE-2020-5238

Hi,

cmark-gfm is affected by CVE-2020-5238 and consequently the R package is also affected.

Best, Dylan

created time in 8 days

issue openeddaissi/MORFEE

Add support for mouse genome

Question from @AhmedArslan

Currently, it need some manual steps.

created time in 14 days

startedaeris/firewall-piercer

started time in 14 days

create barnchdaissi/MORFEE

branch : class

created branch time in 15 days

push eventdaissi/daissi.github.io

Dylan Aïssi

commit sha ad0877ff6168d0aa8ab1f5e8762e40d7f5348149

Add Makefile

view details

Dylan Aïssi

commit sha b74ff930f4a273a99c39621a4370f0970f5762c7

Add DebR logo

view details

push time in 21 days

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 134d030d13da68c73c2fb878b1d14c48538b266c

Update description of xlsx output

view details

push time in 23 days

push eventdaissi/MORFEE

Dylan Aïssi

commit sha d77509071f196e5787276714dd092eebecbd558c

Change column name in output xlsx

view details

push time in 25 days

issue openedaristocratos/bashtop

[BUG] loads Python modules from cwd

Forward of another Debian security bug report by Jakub Wilk (This is similar to https://github.com/aristocratos/bashtop/issues/161, but less severe.)

Describe the bug

bashtop runs

python3 -c "import psutil"

to check if the psutil module is available.

But when you use -c, Python adds the current working directory to the module search path¹. As consequence, you can't run bashtop securely when your cwd is untrusted (e.g. /tmp).

I suggest changing the command in question to:

(cd / && python3 -c "import psutil")

¹ https://docs.python.org/3/using/cmdline.html#cmdoption-c

created time in 25 days

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 4cdcaf0e5cf513fab1918b196cf29b8c7236ff89

Add more info in output

view details

push time in a month

push eventdaissi/daissi.github.io

Dylan Aïssi

commit sha fa19b88b0c53d95d4728ebd4566ff123922a8bd3

Remove description

view details

push time in a month

issue commentaristocratos/bashtop

[BUG] insecure use of /tmp

pytmpdir=$(mktemp -d "${TMPDIR:-/tmp}"/XXXXXXXXXXXX) pywrapper=$(mktemp "${pytmpdir}"/bashtop.psutil.XXXX)

Should fix the issue.

Does the proposed fix by upstream look good to you?

It's mostly OK, but:

  • mktemp(1) can fail, and this failure should not be ignored;
  • there's no need for two mktemp calls.

Something like this should work:

pytmpdir=$(mktemp -d "${TMPDIR:-/tmp}"/bashtop.XXXXXX) || exit 1 pywrapper=${pytmpdir}/psutil

-- Jakub Wilk

daissi

comment created time in a month

issue commentaristocratos/bashtop

[BUG] insecure use of /tmp

Hi Jakub,

Le lun. 6 juil. 2020 à 13:29, aristocratos notifications@github.com a écrit :

pytmpdir=$(mktemp -d "${TMPDIR:-/tmp}"/XXXXXXXXXXXX) pywrapper=$(mktemp "${pytmpdir}"/bashtop.psutil.XXXX)

Should fix the issue.

Does the proposed fix by upstream look good to you?

Best, Dylan

daissi

comment created time in a month

issue openedaristocratos/bashtop

[BUG] insecure use of /tmp

Forward of a Debian bug report

Describe the bug

bashtop creates a Python script in /tmp and runs it. But Python adds the directory containing the script to the module search path¹, and /tmp is world-writable, so this in insecure. A local user could plant malicious Python module in /tmp, which would be executed by bashtop.

To Reproduce

Create a psutil.py file with: import os; os.system('(tput reset && cowsay pwned) >/dev/tty; kill -ABRT %s' % os.getppid())

  $ install -m 644 /path/to/psutil.py /tmp
  $ bashtop
   _______
  < pwned >
   -------
          \   ^__^
           \  (oo)\_______
              (__)\       )\/\
                  ||----w |
                  ||     ||
  Aborted

created time in a month

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 927a3d1f8e544857e1d9f0932fc9515be0b00b58

Improve vcf_2_xlsx for uSTOPs

view details

push time in a month

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 0ccaa7a48aa08bfafacf3e2ca0abc60e653221ce

Test if alleles are A, T, C or G

view details

push time in a month

push eventdaissi/MORFEE

Dylan Aïssi

commit sha af99d943e854ddf2e728fbde00df27abc0808a85

Bump versions

view details

push time in a month

pull request commentwaqasuddinkhan/MACARON-GenMed-LabEx

MACARON update

Hi @FlorianThibord

* GATK4 is not completely silent despite setting QUIET and verbosity parameters. Need to find a way to hide it in the next version...

What about redirect stdout (and/or stderr) to /dev/null? gatk .... > /dev/null 2>&1

Not tested but should do the job!

FlorianThibord

comment created time in a month

issue openedaristocratos/bashtop

[REQUEST] Add support for themes installed system-wide

Is your feature request related to a problem? Please describe. Distrib packagers (at least for Debian/Ubuntu/Fedora) install bashtop themes into /usr/share/bashtop/themes/. But bashtop doesn't look into this folder and doesn't load these themes.

Describe the solution you'd like bashtop should look if there are themes installed system-wide and should be able to load them.

Additional context This feature will avoid to have duplicate theme files on systems with many users.

created time in a month

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 7c01750b787ba44c512a74b513d75c650c7f7b02

Bump version

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 3c51d8866eb0c0b3b827093e84ce77f4681ac240

Initial stop deletion detection

view details

Dylan Aïssi

commit sha d72d027165ac0c6500b89107b99dfe3ef0ba04e9

Initial STOP output

view details

Dylan Aïssi

commit sha 4bcf6e17a247ea4d2f93c75b46fa272c3408d291

Initial detection of uSTOP

view details

Dylan Aïssi

commit sha 7fe384c9dfaed8e32e529007c836213853b3e521

Update uSTOP

view details

Dylan Aïssi

commit sha e3fb1a7ee17d413d0146065a6268418614347098

Finish uSTOP detection

view details

Dylan Aïssi

commit sha 65edfd0584bce09e5e2dbe6848911927f1c15d80

Report which STOP codon is used

view details

Dylan Aïssi

commit sha 27a919a911a1a290895f5c80b1b91e8dbe5edc98

Only use new stop that is AFTER uATG

view details

Dylan Aïssi

commit sha 56fb79c3e1c8dd4b1972909f0ebf8740198e300e

Fix output for uSTOP not in ORF

view details

Dylan Aïssi

commit sha 3b91f6f5b69a0a8fe54149cae0c2d9ac529c61a9

Fix end of line

view details

Dylan Aïssi

commit sha fbd116f8b0f17922df4acde39006c375b4c66c66

Switch other print to message

view details

Dylan Aïssi

commit sha ad2272b70134f2b9a3b9a72c3b6221a907d0d54b

Add debug output

view details

Dylan Aïssi

commit sha 5140652b5aed3f077078ec64f1cb68fd26ee6422

Use predicted and not generated

view details

Dylan Aïssi

commit sha 14dddc5330053ba2bd3b10777fb90f632f681c07

Fix position for used STOP position

view details

Dylan Aïssi

commit sha f21c0131a1b196b572b190e2ab830e4fafbbd817

Use ORF instead protein in output

view details

Dylan Aïssi

commit sha 7454a3fcfebe908c9e765027aafc71a43fec3b75

Skip variants with wrong upstream annotation

view details

Dylan Aïssi

commit sha 6391f34c08ac680c771349f33312605d1ca6d6e2

Initial output for uSTOP

view details

Dylan Aïssi

commit sha 1d85fe051650c77ed4d09c9752712a11e186ab3a

Slip output for uATG and uSTOP

view details

Dylan Aïssi

commit sha 84d71f68df7e29b3e91aba71c1cc6e7cb2dd61a5

Fix vcf_2_xlsx

view details

Dylan Aïssi

commit sha 6fccd22713356954c6b6438516230a2f6ebd0695

Report elongated CDS

view details

Dylan Aïssi

commit sha 4ac0d4032ed9aa0e78e61d8a43af58c732595438

Merge pull request #2 from daissi/stop Add detection of uSTOP deletion

view details

push time in 2 months

PR merged daissi/MORFEE

Add detection of uSTOP deletion
+183 -27

0 comment

3 changed files

daissi

pr closed time in 2 months

PR opened daissi/MORFEE

Add detection of uSTOP deletion
+183 -27

0 comment

3 changed files

pr created time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 6fccd22713356954c6b6438516230a2f6ebd0695

Report elongated CDS

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 1d85fe051650c77ed4d09c9752712a11e186ab3a

Slip output for uATG and uSTOP

view details

Dylan Aïssi

commit sha 84d71f68df7e29b3e91aba71c1cc6e7cb2dd61a5

Fix vcf_2_xlsx

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 6391f34c08ac680c771349f33312605d1ca6d6e2

Initial output for uSTOP

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha d6dfa97d84be34c4e5ad2993bf1cf5504003b5ef

Initial rmarkdown template

view details

Dylan Aïssi

commit sha c6ccb9fcc3844ea8631cbb2477189f5cda66a8f4

Update GH for bioc

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 7454a3fcfebe908c9e765027aafc71a43fec3b75

Skip variants with wrong upstream annotation

view details

push time in 2 months

PR opened daissi/bashtop

Add reference to official Debian/Ubuntu repositories
+4 -0

0 comment

1 changed file

pr created time in 2 months

create barnchdaissi/bashtop

branch : daissi-deb

created branch time in 2 months

fork daissi/bashtop

Linux/OSX/FreeBSD resource monitor

fork in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 5140652b5aed3f077078ec64f1cb68fd26ee6422

Use predicted and not generated

view details

Dylan Aïssi

commit sha 14dddc5330053ba2bd3b10777fb90f632f681c07

Fix position for used STOP position

view details

Dylan Aïssi

commit sha f21c0131a1b196b572b190e2ab830e4fafbbd817

Use ORF instead protein in output

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha ad2272b70134f2b9a3b9a72c3b6221a907d0d54b

Add debug output

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha fbd116f8b0f17922df4acde39006c375b4c66c66

Switch other print to message

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 6f3d7cea20f62da821ff795b505c5e6961915d6a

Fix again some other messages

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 016cccd35c146d3a43db758e0692fd94ab4c6046

Fix other messages

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 3b91f6f5b69a0a8fe54149cae0c2d9ac529c61a9

Fix end of line

view details

Dylan Aïssi

commit sha 597aeb05954810807c4118b09d4e36979eec38d2

Switch other print to message

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 27a919a911a1a290895f5c80b1b91e8dbe5edc98

Only use new stop that is AFTER uATG

view details

Dylan Aïssi

commit sha 56fb79c3e1c8dd4b1972909f0ebf8740198e300e

Fix output for uSTOP not in ORF

view details

push time in 2 months

create barnchdaissi/lintian

branch : 961709

created branch time in 2 months

create barnchdaissi/lintian

branch : buster-backports

created branch time in 2 months

create barnchdaissi/lintian

branch : stretch-backports

created branch time in 2 months

create barnchdaissi/lintian

branch : master

created branch time in 2 months

create barnchdaissi/lintian

branch : README

created branch time in 2 months

create barnchdaissi/lintian

branch : 1.23.0

created branch time in 2 months

create barnchdaissi/lintian

branch : stretch

created branch time in 2 months

create barnchdaissi/lintian

branch : merge-hardening-check

created branch time in 2 months

create barnchdaissi/lintian

branch : jessie

created branch time in 2 months

create barnchdaissi/lintian

branch : ci-run-tests-again

created branch time in 2 months

create barnchdaissi/lintian

branch : vendor-profile

created branch time in 2 months

create barnchdaissi/lintian

branch : etch

created branch time in 2 months

create barnchdaissi/lintian

branch : 1.22.12

created branch time in 2 months

create barnchdaissi/lintian

branch : 1.22.11

created branch time in 2 months

create barnchdaissi/lintian

branch : javascript-lib

created branch time in 2 months

create barnchdaissi/lintian

branch : lenny

created branch time in 2 months

create barnchdaissi/lintian

branch : reporting-rewrite-config-and-archive-handling

created branch time in 2 months

create barnchdaissi/lintian

branch : pre2.6.25

created branch time in 2 months

create barnchdaissi/lintian

branch : tag-non-official-wording

created branch time in 2 months

create barnchdaissi/lintian

branch : squeeze

created branch time in 2 months

create barnchdaissi/lintian

branch : wheezy

created branch time in 2 months

created repositorydaissi/lintian

created time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 65edfd0584bce09e5e2dbe6848911927f1c15d80

Report which STOP codon is used

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha e3fb1a7ee17d413d0146065a6268418614347098

Finish uSTOP detection

view details

push time in 2 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 3c51d8866eb0c0b3b827093e84ce77f4681ac240

Initial stop deletion detection

view details

Dylan Aïssi

commit sha d72d027165ac0c6500b89107b99dfe3ef0ba04e9

Initial STOP output

view details

Dylan Aïssi

commit sha 4bcf6e17a247ea4d2f93c75b46fa272c3408d291

Initial detection of uSTOP

view details

Dylan Aïssi

commit sha 7fe384c9dfaed8e32e529007c836213853b3e521

Update uSTOP

view details

push time in 2 months

startedjuliagoda/antimicroX

started time in 3 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 4afd2ba6412700ffaac33b19dd35f84668a3240d

Add GH for bioc

view details

push time in 3 months

push eventdaissi/MORFEE

Dylan Aïssi

commit sha 36c2110f0c615de492b2ea0b3972bfb5b382c90a

Support chr annotation with "chr" prefix

view details

push time in 3 months

startedventoy/Ventoy

started time in 3 months

issue commentimbs-hl/ranger

Testsuite fails on some architectures (arm64, ppc64el and s390x)

I had private discussion with Jeroen about the support of Travis for non-amd64 arches. No work in this direction is planned as the R community is moving away from Travis in favor to GitHub Actions. Maybe in some future, we will be able to enable GH for non-amd64 arches.

Back to our issue, the regression is due to the increase of num.trees there:

https://github.com/imbs-hl/ranger/blob/5151df0bc10531cceaa278fccf7b6ab9324e5103/tests/testthat/test_maxstat.R#L39

It works fine up to num.trees=20, it starts to fail with 21, at least on an ARM64 Debian porterbox.

daissi

comment created time in 3 months

more