John Marshall
@johnm.bsky.social
Bioinformatics tools developer at Australia’s Centre for Population Genomics. Will edit GA4GH specifications for food. New Zealander fairly recently returned after a decade in the U.K.
Me, I dislike this setting. Commit messages explain a change for posterity; PR descriptions also introduce the change (and its author, for new contributors) and explain why the maintainers should be motivated to merge it now. These texts can need to be different, as their audiences and roles differ.
TIL this setting on GitHub. kinda mad about the years of git commits could have contained my beautiful PR descriptions
February 15, 2026 at 1:32 AM
Me, I dislike this setting. Commit messages explain a change for posterity; PR descriptions also introduce the change (and its author, for new contributors) and explain why the maintainers should be motivated to merge it now. These texts can need to be different, as their audiences and roles differ.
“I previously noticed that the Conda version of samtools does not support the interactive tview command.”
In fact bioconda's samtools has supported tview for the last eight years.
“Yes, I've heard that previous Conda versions of samtools had this issue, but I haven't tested the latest one…”
In fact bioconda's samtools has supported tview for the last eight years.
“Yes, I've heard that previous Conda versions of samtools had this issue, but I haven't tested the latest one…”
Curses library issues when compiling samtools · Issue #2303 · samtools/samtools
I previously noticed that the Conda version of samtools does not support the interactive tview command. However, even after compiling the latest version (v1.23) from source, the resulting binary st...
github.com
February 9, 2026 at 9:44 PM
“I previously noticed that the Conda version of samtools does not support the interactive tview command.”
In fact bioconda's samtools has supported tview for the last eight years.
“Yes, I've heard that previous Conda versions of samtools had this issue, but I haven't tested the latest one…”
In fact bioconda's samtools has supported tview for the last eight years.
“Yes, I've heard that previous Conda versions of samtools had this issue, but I haven't tested the latest one…”
Reposted by John Marshall
a nice thing about when the internet was a bunch of little sites and servers was that it was a lot harder for governments to pressure "the chat provider everyone uses" to implement age verification.
you wanna pressure 300 separate IRC servers? good luck with that. but one company? easy
you wanna pressure 300 separate IRC servers? good luck with that. but one company? easy
February 9, 2026 at 8:00 PM
a nice thing about when the internet was a bunch of little sites and servers was that it was a lot harder for governments to pressure "the chat provider everyone uses" to implement age verification.
you wanna pressure 300 separate IRC servers? good luck with that. but one company? easy
you wanna pressure 300 separate IRC servers? good luck with that. but one company? easy
Reposted by John Marshall
The consequences curve is now so sharp companies can do the finding out months before they fuck around
February 9, 2026 at 7:17 PM
The consequences curve is now so sharp companies can do the finding out months before they fuck around
Reposted by John Marshall
/me SCREAMS IN NORWEGIAN SOVEREIGN WEALTH FUND
Breaking: the Government is negotiating with the US to provide access to our critical minerals, while a memo before the Waitangi Tribunal says a backdoor deal violates obligations to Māori
NZ in talks with US on Trump minerals deal
newsroom.co.nz
January 30, 2026 at 4:02 AM
/me SCREAMS IN NORWEGIAN SOVEREIGN WEALTH FUND
Dear open-source maintainer,
Please expend effort to support a platform that is of no interest to you or the bulk of your project's user base, because “that's where the majority of the non-[your project's audience] user base lies”.
Please expend effort to support a platform that is of no interest to you or the bulk of your project's user base, because “that's where the majority of the non-[your project's audience] user base lies”.
Install of pysam on win64 · Issue #1375 · pysam-developers/pysam
Have been trying to do the above using Cygwin. Found it very frustrating to a point of trying to rebuild the binaries from the repository and drilling down to rebuilding htslib and the associated t...
github.com
January 28, 2026 at 9:00 PM
Dear open-source maintainer,
Please expend effort to support a platform that is of no interest to you or the bulk of your project's user base, because “that's where the majority of the non-[your project's audience] user base lies”.
Please expend effort to support a platform that is of no interest to you or the bulk of your project's user base, because “that's where the majority of the non-[your project's audience] user base lies”.
Reposted by John Marshall
A few years ago I learned the history behind this photograph. it was taken by a soldier in Nazi occupied Sarajevo, the Muslim woman is using her veil to cover the yellow star of the Jewish woman behind her. But there's so much more to the story
January 28, 2026 at 8:11 PM
A few years ago I learned the history behind this photograph. it was taken by a soldier in Nazi occupied Sarajevo, the Muslim woman is using her veil to cover the yellow star of the Jewish woman behind her. But there's so much more to the story
I went “hooray!!” out loud.
With the possible exception of the Law Commission bit.
(To be clear, I am an equal-opportunities disparager, and will be even happier when Luxo and that prick Seymour put themselves out to pasture.)
With the possible exception of the Law Commission bit.
(To be clear, I am an equal-opportunities disparager, and will be even happier when Luxo and that prick Seymour put themselves out to pasture.)
January 27, 2026 at 10:29 PM
I went “hooray!!” out loud.
With the possible exception of the Law Commission bit.
(To be clear, I am an equal-opportunities disparager, and will be even happier when Luxo and that prick Seymour put themselves out to pasture.)
With the possible exception of the Law Commission bit.
(To be clear, I am an equal-opportunities disparager, and will be even happier when Luxo and that prick Seymour put themselves out to pasture.)
In truth… from time to time — especially when travelling — I used to telnet into port 110 and type POP3 commands by hand to have a basic look at any new email.
January 26, 2026 at 9:27 PM
In truth… from time to time — especially when travelling — I used to telnet into port 110 and type POP3 commands by hand to have a basic look at any new email.
Reposted by John Marshall
Rutte:
-slaps top of existing arrangement relating to US presence in Greenland-
"This bad boy can fit so many US military bases and whatever the fuck Golden Dome is in it!"
Trump:
"I'll take it! Art of the deal, baby!"
-slaps top of existing arrangement relating to US presence in Greenland-
"This bad boy can fit so many US military bases and whatever the fuck Golden Dome is in it!"
Trump:
"I'll take it! Art of the deal, baby!"
January 21, 2026 at 8:39 PM
Rutte:
-slaps top of existing arrangement relating to US presence in Greenland-
"This bad boy can fit so many US military bases and whatever the fuck Golden Dome is in it!"
Trump:
"I'll take it! Art of the deal, baby!"
-slaps top of existing arrangement relating to US presence in Greenland-
"This bad boy can fit so many US military bases and whatever the fuck Golden Dome is in it!"
Trump:
"I'll take it! Art of the deal, baby!"
Reposted by John Marshall
A number of people on this platform have been claiming that it's not up to government to shorten people's time on remand, however far beyond the statutory limit that time extends.
Well, take it from a very eminent retired judge. It is.
www.theguardian.com/uk-news/2026...
Well, take it from a very eminent retired judge. It is.
www.theguardian.com/uk-news/2026...
Palestine Action hunger strikers are still the state’s responsibility | Letters
Letters: The power is in the hands of the DPP or the attorney general, writes Stephen Sedley. Plus Roshi Fernando on Keir Starmer’s unforgivable conduct
www.theguardian.com
January 13, 2026 at 7:44 AM
A number of people on this platform have been claiming that it's not up to government to shorten people's time on remand, however far beyond the statutory limit that time extends.
Well, take it from a very eminent retired judge. It is.
www.theguardian.com/uk-news/2026...
Well, take it from a very eminent retired judge. It is.
www.theguardian.com/uk-news/2026...
Reposted by John Marshall
This is interesting because when I went for my first Covid vaccination, Farage arrived and pushed straight to the front of the queue.
Farage: "I believe in vaccinations when they're vaccinations. I don't think what happened with Covid were vaccinations. You have to keep having them every 6 months."
Conspiratorial nonsense.
Some vaccinations like Covid shots require multiple/seasonal doses because immunity fades & viruses change.
Conspiratorial nonsense.
Some vaccinations like Covid shots require multiple/seasonal doses because immunity fades & viruses change.
January 7, 2026 at 8:52 PM
This is interesting because when I went for my first Covid vaccination, Farage arrived and pushed straight to the front of the queue.
My interest in and level of caring about UK politics has decreased in the three years since I left the UK. But I care about this. Today I've written to Starmer and Lammy imploring them to act, and written to my former MP. If you're in the UK, I hope you will too.
If the Palestine Action hunger strikers die - which they could do at any moment, as they are now very close to the end - it will be the government that killed them. Today’s column explains why. Please share, and write urgently to your MP.
www.theguardian.com/commentisfre...
www.theguardian.com/commentisfre...
Let’s be clear: if the Palestine Action hunger strikers die, the government will bear moral responsibility | George Monbiot
The three remaining hunger strikers have been convicted of nothing. Yet with astonishing cruelty, ministers refuse to listen to their reasonable demands, says Guardian columnist George Monbiot
www.theguardian.com
January 7, 2026 at 10:48 AM
My interest in and level of caring about UK politics has decreased in the three years since I left the UK. But I care about this. Today I've written to Starmer and Lammy imploring them to act, and written to my former MP. If you're in the UK, I hope you will too.
At a first glance, you might think Calvin's bike maintenance videos are going to be boring. But you rapidly realise his knowledge of the craft is incredible, his ability to clearly explain it is unsurpassed, and there's just the right amount of dry humour in there.
Context for those not involved in cycling: this is basically the same as Bob Ross or Mr Rogers retiring. Calvin has been a fixture of bike mechanic content for my entire adult life. www.parktool.com/en-int/blog/... #cycling #bikes
Calvin Jones Retiring After 28 Years As Director of Education at Park…
Park Tool has been manufacturing bicycle specific tools since 1963. Based out of St. Paul Minnesota, we are the world's largest bicycle tool manufacturer. A long-term dedication to quality,…
www.parktool.com
January 6, 2026 at 6:38 PM
At a first glance, you might think Calvin's bike maintenance videos are going to be boring. But you rapidly realise his knowledge of the craft is incredible, his ability to clearly explain it is unsurpassed, and there's just the right amount of dry humour in there.
Couldn't see any #ManageMyHealth 2FA UI before today, but now I can and have set it up. The enrolment flow seems mostly competently done (surprisingly) and it's now active on my account. Except:
• the iOS app doesn't bother checking 2FA 🤷
• recovery codes mix 1 and letter I in the same positions 🙄
• the iOS app doesn't bother checking 2FA 🤷
• recovery codes mix 1 and letter I in the same positions 🙄
January 6, 2026 at 6:53 AM
Couldn't see any #ManageMyHealth 2FA UI before today, but now I can and have set it up. The enrolment flow seems mostly competently done (surprisingly) and it's now active on my account. Except:
• the iOS app doesn't bother checking 2FA 🤷
• recovery codes mix 1 and letter I in the same positions 🙄
• the iOS app doesn't bother checking 2FA 🤷
• recovery codes mix 1 and letter I in the same positions 🙄
Reposted by John Marshall
Pretty textbook on how not to do crisis communication for this type of attack. So here’s a little thread on what to do instead. 🧵
If you don’t know, I’m Hadyn Green, Principal Communications advisor at @first.org and my job is to go around the world teaching people how to do to cybersecurity comms
If you don’t know, I’m Hadyn Green, Principal Communications advisor at @first.org and my job is to go around the world teaching people how to do to cybersecurity comms
Manage My Health CEO: 'Trust us even though we've dropped the ball'
The chief executive of beleaguered patient portal says he is open to standing down if required.
www.rnz.co.nz
January 6, 2026 at 6:15 AM
Pretty textbook on how not to do crisis communication for this type of attack. So here’s a little thread on what to do instead. 🧵
If you don’t know, I’m Hadyn Green, Principal Communications advisor at @first.org and my job is to go around the world teaching people how to do to cybersecurity comms
If you don’t know, I’m Hadyn Green, Principal Communications advisor at @first.org and my job is to go around the world teaching people how to do to cybersecurity comms
Reposted by John Marshall
As one last bit of trivia, apparently "Kazu" also read my blog post.
It also means that my Telegram pseudonym is blown but I had signalled to them explicitly what I would make public so I don't have any reason to think they'd go after me.
It also means that my Telegram pseudonym is blown but I had signalled to them explicitly what I would make public so I don't have any reason to think they'd go after me.
January 5, 2026 at 8:19 PM
As one last bit of trivia, apparently "Kazu" also read my blog post.
It also means that my Telegram pseudonym is blown but I had signalled to them explicitly what I would make public so I don't have any reason to think they'd go after me.
It also means that my Telegram pseudonym is blown but I had signalled to them explicitly what I would make public so I don't have any reason to think they'd go after me.
Reposted by John Marshall
This is particularly interesting (if you’re a nerd) because the plot you get at the end tells you a lot about the relative usefulness of different terms.
Will genuinely try to adjust how I write in line with them (especially if the sample size gets bigger).
Will genuinely try to adjust how I write in line with them (especially if the sample size gets bigger).
How likely is ‘likely’? Does ‘likely’ have a higher probability than ‘probable’? I put together a quick quiz so you can see how you interpret probability phrases, then see how you compare with others: probability.kucharski.io
January 5, 2026 at 3:47 PM
This is particularly interesting (if you’re a nerd) because the plot you get at the end tells you a lot about the relative usefulness of different terms.
Will genuinely try to adjust how I write in line with them (especially if the sample size gets bigger).
Will genuinely try to adjust how I write in line with them (especially if the sample size gets bigger).
Reposted by John Marshall
🚨🚨I'll be speaking to @catheriner.bsky.social today about Venezuela on my podcast. She was Britain's ambassador to Venezuela and met Chavez and Maduro. So, somebody who actually knows this subject intimately!🚨🚨
Episode should be out late tonight. Watch this space:
podcasts.apple.com/gb/podcast/b...
Episode should be out late tonight. Watch this space:
podcasts.apple.com/gb/podcast/b...
Behind The Lines with Arthur Snell
Politics Podcast · Updated weekly · Behind the Lines with Arthur Snell is a geopolitics podcast. Every week we give the listener access to the best informed people to help you understand this turbule...
podcasts.apple.com
January 4, 2026 at 5:54 PM
🚨🚨I'll be speaking to @catheriner.bsky.social today about Venezuela on my podcast. She was Britain's ambassador to Venezuela and met Chavez and Maduro. So, somebody who actually knows this subject intimately!🚨🚨
Episode should be out late tonight. Watch this space:
podcasts.apple.com/gb/podcast/b...
Episode should be out late tonight. Watch this space:
podcasts.apple.com/gb/podcast/b...
Reposted by John Marshall
WGSをbwa-mem2でマッピングする際、パイプを使って特定の配列にのみアラインメントされた結果を取り出すのに一苦労。
通常のBAMファイルみたいにsamtools viewで取り出そうとすると「ランダムアクセスはindexが必要（つまり一旦ファイルにする必要がある）」
同じsamtools viewでもexpressionによるフィルタリングで取り出せる。
通常のBAMファイルみたいにsamtools viewで取り出そうとすると「ランダムアクセスはindexが必要（つまり一旦ファイルにする必要がある）」
同じsamtools viewでもexpressionによるフィルタリングで取り出せる。
January 4, 2026 at 9:21 AM
WGSをbwa-mem2でマッピングする際、パイプを使って特定の配列にのみアラインメントされた結果を取り出すのに一苦労。
通常のBAMファイルみたいにsamtools viewで取り出そうとすると「ランダムアクセスはindexが必要（つまり一旦ファイルにする必要がある）」
同じsamtools viewでもexpressionによるフィルタリングで取り出せる。
通常のBAMファイルみたいにsamtools viewで取り出そうとすると「ランダムアクセスはindexが必要（つまり一旦ファイルにする必要がある）」
同じsamtools viewでもexpressionによるフィルタリングで取り出せる。
Three years to get a one-line change into conda… 💀
`conda run` adds an extra newline to the output · Issue #11763 · conda/conda
Checklist I added a descriptive title I searched open reports and couldn't find a duplicate What happened? Running a command via conda run adds an extra newline (when the output is non-empty): (bas...
github.com
December 22, 2025 at 8:53 PM
Three years to get a one-line change into conda… 💀
Reposted by John Marshall
THREAD.
My parents' cat Bridget vanished. As the weeks dragged on they became ever more worried, so to distract himself my dad began to paint Bridget's adventures, imagining her travelling through time and popping up at some of art & music's most important moments.
I've collected his work here...
My parents' cat Bridget vanished. As the weeks dragged on they became ever more worried, so to distract himself my dad began to paint Bridget's adventures, imagining her travelling through time and popping up at some of art & music's most important moments.
I've collected his work here...
December 20, 2025 at 9:21 AM
THREAD.
My parents' cat Bridget vanished. As the weeks dragged on they became ever more worried, so to distract himself my dad began to paint Bridget's adventures, imagining her travelling through time and popping up at some of art & music's most important moments.
I've collected his work here...
My parents' cat Bridget vanished. As the weeks dragged on they became ever more worried, so to distract himself my dad began to paint Bridget's adventures, imagining her travelling through time and popping up at some of art & music's most important moments.
I've collected his work here...
Reposted by John Marshall
SAMtools / HTSLib / BCFTools 1.23 has been released. See the releasenotes on GitHub and www.htslib.org for details.
Samtools
Samtools
www.htslib.org
December 16, 2025 at 3:33 PM
SAMtools / HTSLib / BCFTools 1.23 has been released. See the releasenotes on GitHub and www.htslib.org for details.
Reposted by John Marshall
why the fuck isn't the government pouring money into and emergency response to this??
OK, Tāmaki Makaurau, the hornet army is on the march. Time to saddle up, cut up some bottles and trap the little bastards before they do any more damage.
MPI has bumped up the zone so if you're inside that purple line it's time to get busy.
More info here: www.mpi.govt.nz/news/media-r...
MPI has bumped up the zone so if you're inside that purple line it's time to get busy.
More info here: www.mpi.govt.nz/news/media-r...
December 14, 2025 at 8:11 PM
why the fuck isn't the government pouring money into and emergency response to this??
Reposted by John Marshall
A quick social media ban story. Junior Cans' best mate moved to the North Island in April. He talks with him every day on Facebook messenger. They play Minecraft together, and runs a voice chat. When I moved house as a kid, those friendships pretty much ended. His hasn't.
December 11, 2025 at 8:50 PM
A quick social media ban story. Junior Cans' best mate moved to the North Island in April. He talks with him every day on Facebook messenger. They play Minecraft together, and runs a voice chat. When I moved house as a kid, those friendships pretty much ended. His hasn't.