It seems to me seg-based filtering or low-complexity regions in BLAST cannot work. I see using: $ strings /usr/bin/blastpgp | less [cut] BLASTFILTER seg %s%s%s%s%s /usr/ncbi/blast/filter Call to seg failed. ^z $ ls -la /usr/ncbi/blast/filter ls: cannot access /usr/ncbi/blast/filter: No such file or directory $ ls -la /usr/share/ncbi total 16 drwxr-xr-x 4 root root 4096 Apr 18 2008 . drwxr-xr-x 139 root root 4096 Dec 2 03:56 .. drwxr-xr-x 2 root root 4096 Dec 2 02:03 data drwxr-xr-x 2 root root 4096 Apr 18 2008 formatdb $
(In reply to comment #0) > It seems to me seg-based filtering or low-complexity regions in BLAST cannot ------------of (was a typo, sorry) > work. I see using:
So what should we do here? There are no filter installed. What does upstream intend? Do one need to download them seperately?
The bug has been closed via the following commit(s): https://gitweb.gentoo.org/repo/gentoo.git/commit/?id=59b2be273d92b67c4c7f581657151a5e7cbb63ae commit 59b2be273d92b67c4c7f581657151a5e7cbb63ae Author: Jakov Smolić <jsmolic@gentoo.org> AuthorDate: 2021-08-30 17:17:23 +0000 Commit: Jakov Smolić <jsmolic@gentoo.org> CommitDate: 2021-08-30 17:38:50 +0000 sci-biology/ncbi-tools: Remove last-rited package Closes: https://bugs.gentoo.org/649930 Closes: https://bugs.gentoo.org/782790 Closes: https://bugs.gentoo.org/741188 Closes: https://bugs.gentoo.org/715636 Closes: https://bugs.gentoo.org/710338 Closes: https://bugs.gentoo.org/701340 Closes: https://bugs.gentoo.org/586982 Closes: https://bugs.gentoo.org/295584 Signed-off-by: Jakov Smolić <jsmolic@gentoo.org> profiles/package.mask | 6 - sci-biology/ncbi-tools/Manifest | 1 - sci-biology/ncbi-tools/files/21ncbi-r1 | 6 - .../files/ncbi-tools-2.2.26-_DEFAULT_SOURCE.patch | 81 ---------- .../files/ncbi-tools-2.2.26-bfr-overflow.patch | 103 ------------- .../files/ncbi-tools-2.2.26-format-security.patch | 124 --------------- .../ncbi-tools/files/ncbi-tools-extra_vib.patch | 37 ----- sci-biology/ncbi-tools/files/ncbi-tools-lop.patch | 15 -- sci-biology/ncbi-tools/files/ncbirc | 2 - sci-biology/ncbi-tools/metadata.xml | 8 - sci-biology/ncbi-tools/ncbi-tools-2.2.26-r3.ebuild | 169 --------------------- 11 files changed, 552 deletions(-)
It is still developed, see https://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2021/Aug_18_2021/README.html , albeit in c++. However, for those of use who have issues on some hosts to get that compiled, we were happy to use an older implementation in C. Why didn't you just just go the --without-x or --disable-x way? Why dropping the whole bundle? Please restore the package.
(In reply to Martin Mokrejš from comment #4) > It is still developed, see > https://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/ARCHIVE/2021/Aug_18_2021/ > README.html , albeit in c++. However, for those of use who have issues on > some hosts to get that compiled, we were happy to use an older > implementation in C. > > Why didn't you just just go the --without-x or --disable-x way? Why dropping > the whole bundle? > > Please restore the package. Please see https://bugs.gentoo.org/701340#c13
