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HenrikBengtsson / CBI-software

A Scientific Software Stack for HPC (CentOS oriented)
https://wynton.ucsf.edu/hpc/software/software-repositories.html
5 stars 2 forks source link

User request for older star version #40

Closed hgputnam closed 2 years ago

hgputnam commented 2 years ago

Not sure if this is the correct place for this or if I should post on c4-sysadmin? At any rate, one of our C4 users is asking for a prior verison:

Hi Harry, I tried to run star on the server, and ran into this error. EXITING because of FATAL ERROR: Genome version: 20201 is INCOMPATIBLE with running STAR version: 2.7.5a SOLUTION: please re-generate genome from scratch with running version of STAR, or with version: 2.7.4a will you consider install a lower version on the server.

hgputnam commented 2 years ago

So, I think she wants the 2.74a version.

hgputnam commented 2 years ago

User says she can regenerate the genome. Out of curiosity, how much work is it to do something like this?

HenrikBengtsson commented 2 years ago

Installed on C4:

module load CBI
module avail star

------------------------ /software/c4/cbi/modulefiles -------------------------
   star/2.7.4a    star/2.7.5c    star/2.7.9a (D)
   star/2.7.5a    star/2.7.7a

... Out of curiosity, how much work is it to do something like this?

For this one, it's super easy. All I need to do is, on a dev node, go to the folder where I've cloned this repo and do:

[henrik@c4-dev3 CBI-software]$ CBI/star
[henrik@c4-dev3 star]$ make VERSION=2.7.4.a

This will download, extract, configure, make, make install, and install the module, and validate that the module can be loaded in one call.

Output details 
Makefile:16: warning: overriding recipe for target '/software/c4/cbi/software/STAR-2.7.4a/bin/Linux_x86_64/STAR'
../utils.mk:195: warning: ignoring old recipe for target '/software/c4/cbi/software/STAR-2.7.4a/bin/Linux_x86_64/STAR'
NAME: STAR
VERSION: 2.7.4a
VERSION_X_Y_Z: 2.7.4
VERSION_X_Y: 2.7
VERSION_X: 2
VERSION_Y: 7
URL: 

CORE:
TMPDIR*: /scratch/henrik
BUILD_HOME: /scratch/henrik/20220215
BUILD_NAME: STAR-2.7.4a
BUILD_PATH: /scratch/henrik/20220215/STAR-2.7.4a

DOWNLOADING:
DOWNLOAD: true
TARBALL*: STAR_linux-v2.7.4a.tar.gz
DOWNLOAD_PATH: /scratch/henrik/20220215/STAR-2.7.4a
DOWNLOAD_TARGET_FILE: bin/Linux_x86_64/STAR
DOWNLOAD_TARGET: /scratch/henrik/20220215/STAR-2.7.4a/bin/Linux_x86_64/STAR

CONFIGURE:
CONFIG: false
CONFIG_OPTS*: 
CONFIG_TARGET_FILE: 
CONFIG_TARGET: 
CONFIG_MODULES: 

BUILDING:
BUILD: false
BUILD_SUFFIX*: 
BUILD_TARGET_FILE: 
BUILD_TARGET: 
BUILD_MODULES: 

INSTALLATION:
INSTALL: true
INSTALL_TARGET: /software/c4/cbi/software/STAR-2.7.4a/bin/Linux_x86_64/STAR
SOFTWARE_HOME: /software/c4/cbi/software
PREFIX: /software/c4/cbi/software/STAR-2.7.4a

MODULES:
MODULE_HOME: /software/c4/cbi/modulefiles
MODULE_NAME: star
MODULE_VERSION: 2.7.4a
MODULE_NAME_VERSION: star/2.7.4a
FULLNAME: STAR-2.7.4a
MODULE_TARGET: /software/c4/cbi/modulefiles/star/2.7.4a.lua
mkdir -p /scratch/henrik/20220215; \
cd /scratch/henrik/20220215; \
curl -L -O https://github.com/alexdobin/STAR/archive/2.7.4a.zip; \
unzip 2.7.4a.zip
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
100   129  100   129    0     0    296      0 --:--:-- --:--:-- --:--:--   296
  0     0    0 8506k    0     0  3553k      0 --:--:--  0:00:02 --:--:-- 5946k
Archive:  2.7.4a.zip
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  inflating: STAR-2.7.4a/source/htslib/cram/zfio.h  
  inflating: STAR-2.7.4a/source/htslib/faidx.5  
  inflating: STAR-2.7.4a/source/htslib/faidx.c  
  inflating: STAR-2.7.4a/source/htslib/hfile.c  
  inflating: STAR-2.7.4a/source/htslib/hfile_internal.h  
  inflating: STAR-2.7.4a/source/htslib/hfile_net.c  
  inflating: STAR-2.7.4a/source/htslib/hts.c  
  inflating: STAR-2.7.4a/source/htslib/htslib.mk  
   creating: STAR-2.7.4a/source/htslib/htslib/
  inflating: STAR-2.7.4a/source/htslib/htslib/bgzf.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/faidx.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/hfile.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/hts.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/hts_defs.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/kfunc.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/khash.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/khash_str2int.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/klist.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/knetfile.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/kseq.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/ksort.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/kstdint.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/kstring.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/sam.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/synced_bcf_reader.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/tbx.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/vcf.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/vcf_sweep.h  
  inflating: STAR-2.7.4a/source/htslib/htslib/vcfutils.h  
  inflating: STAR-2.7.4a/source/htslib/htslib_vars.mk  
  inflating: STAR-2.7.4a/source/htslib/kfunc.c  
  inflating: STAR-2.7.4a/source/htslib/knetfile.c  
  inflating: STAR-2.7.4a/source/htslib/kstring.c  
  inflating: STAR-2.7.4a/source/htslib/sam.5  
  inflating: STAR-2.7.4a/source/htslib/sam.c  
  inflating: STAR-2.7.4a/source/htslib/synced_bcf_reader.c  
  inflating: STAR-2.7.4a/source/htslib/tabix.1  
  inflating: STAR-2.7.4a/source/htslib/tabix.c  
  inflating: STAR-2.7.4a/source/htslib/tbx.c  
  inflating: STAR-2.7.4a/source/htslib/vcf.5  
  inflating: STAR-2.7.4a/source/htslib/vcf.c  
  inflating: STAR-2.7.4a/source/htslib/vcf_sweep.c  
  inflating: STAR-2.7.4a/source/htslib/vcfutils.c  
  inflating: STAR-2.7.4a/source/insertSeqSA.cpp  
  inflating: STAR-2.7.4a/source/insertSeqSA.h  
  inflating: STAR-2.7.4a/source/loadGTF.cpp  
  inflating: STAR-2.7.4a/source/loadGTF.h  
  inflating: STAR-2.7.4a/source/mapThreadsSpawn.cpp  
  inflating: STAR-2.7.4a/source/mapThreadsSpawn.h  
  inflating: STAR-2.7.4a/source/outputSJ.cpp  
  inflating: STAR-2.7.4a/source/outputSJ.h  
  inflating: STAR-2.7.4a/source/parametersDefault  
  inflating: STAR-2.7.4a/source/parametersDefault.xxd  
  inflating: STAR-2.7.4a/source/readLoad.cpp  
  inflating: STAR-2.7.4a/source/readLoad.h  
  inflating: STAR-2.7.4a/source/serviceFuns.cpp  
  inflating: STAR-2.7.4a/source/signalFromBAM.cpp  
  inflating: STAR-2.7.4a/source/signalFromBAM.h  
  inflating: STAR-2.7.4a/source/sjAlignSplit.cpp  
  inflating: STAR-2.7.4a/source/sjdbBuildIndex.cpp  
  inflating: STAR-2.7.4a/source/sjdbBuildIndex.h  
  inflating: STAR-2.7.4a/source/sjdbInsertJunctions.cpp  
  inflating: STAR-2.7.4a/source/sjdbInsertJunctions.h  
  inflating: STAR-2.7.4a/source/sjdbLoadFromFiles.cpp  
  inflating: STAR-2.7.4a/source/sjdbLoadFromFiles.h  
  inflating: STAR-2.7.4a/source/sjdbLoadFromStream.cpp  
  inflating: STAR-2.7.4a/source/sjdbLoadFromStream.h  
  inflating: STAR-2.7.4a/source/sjdbPrepare.cpp  
  inflating: STAR-2.7.4a/source/sjdbPrepare.h  
  inflating: STAR-2.7.4a/source/sortSuffixesBucket.h  
  inflating: STAR-2.7.4a/source/stitchAlignToTranscript.cpp  
  inflating: STAR-2.7.4a/source/stitchAlignToTranscript.h  
  inflating: STAR-2.7.4a/source/stitchGapIndel.cpp  
  inflating: STAR-2.7.4a/source/stitchWindowAligns.cpp  
  inflating: STAR-2.7.4a/source/stitchWindowAligns.h  
  inflating: STAR-2.7.4a/source/streamFuns.cpp  
  inflating: STAR-2.7.4a/source/streamFuns.h  
  inflating: STAR-2.7.4a/source/stringSubstituteAll.cpp  
  inflating: STAR-2.7.4a/source/stringSubstituteAll.h  
  inflating: STAR-2.7.4a/source/sysRemoveDir.cpp  
  inflating: STAR-2.7.4a/source/sysRemoveDir.h  
mkdir -p /software/c4/cbi/software/STAR-2.7.4a
cp -R /scratch/henrik/20220215/STAR-2.7.4a /software/c4/cbi/software/STAR-2.7.4a/..
make post_install
make[1]: Entering directory '/c4/home/henrik/repositories/CBI-software/CBI/star'
Makefile:16: warning: overriding recipe for target '/software/c4/cbi/software/STAR-2.7.4a/bin/Linux_x86_64/STAR'
../utils.mk:195: warning: ignoring old recipe for target '/software/c4/cbi/software/STAR-2.7.4a/bin/Linux_x86_64/STAR'
make[1]: Nothing to be done for 'post_install'.
make[1]: Leaving directory '/c4/home/henrik/repositories/CBI-software/CBI/star'
ls -la /software/c4/cbi/software/STAR-2.7.4a
total 104
drwxr-xr-x   7 henrik cbc   329 Feb 15 11:35 .
drwxr-xr-x 221 henrik cbc  8192 Feb 15 11:35 ..
drwxr-xr-x   5 henrik cbc    90 Feb 15 11:35 bin
-rw-r--r--   1 henrik cbc 32383 Feb 15 11:35 CHANGES.md
-rw-r--r--   1 henrik cbc  3346 Feb 15 11:35 CODE_OF_CONDUCT.md
-rw-r--r--   1 henrik cbc    25 Feb 15 11:35 _config.yml
-rw-r--r--   1 henrik cbc  5795 Feb 15 11:35 CONTRIBUTING.md
drwxr-xr-x   2 henrik cbc    36 Feb 15 11:35 doc
drwxr-xr-x   2 henrik cbc    33 Feb 15 11:35 docs
drwxr-xr-x   5 henrik cbc    68 Feb 15 11:35 extras
-rw-r--r--   1 henrik cbc   210 Feb 15 11:35 .gitignore
-rw-r--r--   1 henrik cbc     0 Feb 15 11:35 .gitmodules
-rw-r--r--   1 henrik cbc  1072 Feb 15 11:35 LICENSE
-rw-r--r--   1 henrik cbc  3240 Feb 15 11:35 README.md
-rw-r--r--   1 henrik cbc 15253 Feb 15 11:35 RELEASEnotes.md
drwxr-xr-x   3 henrik cbc  8192 Feb 15 11:35 source
-rw-r--r--   1 henrik cbc   273 Feb 15 11:35 .travis.yml
SOFTWARE INSTALLED TO: /software/c4/cbi/software/STAR-2.7.4a
mkdir -p "/software/c4/cbi/modulefiles/star"
cp "module.lua.tmpl" "/software/c4/cbi/modulefiles/star/2.7.4a.lua"
module --ignore-cache show star/2.7.4a
----------------------------------------------------------------------------------------------------------------
   /software/c4/cbi/modulefiles/star/2.7.4a.lua:
----------------------------------------------------------------------------------------------------------------
help([[STAR: Spliced Transcripts Alignment to a Reference]])
whatis("Version: 2.7.4a")
whatis("Keywords: sequencing")
whatis("URL: https://github.com/alexdobin/STAR, https://github.com/alexdobin/STAR/blob/master/CHANGES.md (changelog)
")
whatis("Description: STAR (Spliced Transcripts Alignment to a Reference) is a fast NGS read aligner for RNA-seq data
.
Example: `STAR --help`.
")
prepend_path("PATH","/software/c4/cbi/software/STAR-2.7.4a/bin/Linux_x86_64_static")

module load CBI
module load star/2.7.4a
module unload star/2.7.4a

If you would like to try this yourself, I suggest you try it with your own Linux account. I documented the process in the README a few weeks ago. To install to the CBI stack on C4, you'll have to have group write permission to the CBI software and module folders. But for now, I suggest that you try to install your own local version of the CBI stack. I do that all the time on my Linux laptop because I need some of those tools locally.

hgputnam commented 2 years ago

OK, thanks!